gebhart/patrepeval huggingface dataset:
Pathogenesis of Human Reactive-Appearing «Non-Monomorphous» Malignant Lymphoproliferative Disorders: A Hypothesis (1992)

Human reactive-appearing "non-monomorphous" malignant disorders, such as Hodgkin's disease, T-cell-rich B-cell lymphomas and angioimmunoblastic lymphadenopathy display a peculiar and unifying characteristic, which biologically differentiates them from "monomorphous" non-Hodgkin's lymphomas. It consists in the coexistence within the pathologic tissue of a polyclonal, normal-appearing, presumed reactive cellular component, mainly composed of T-lymphocytes together with a clonal cell component constituting a minority of the pathologic mass. To explain the long-lasting coexistence of such polymorphic cell populations in the pathologic tissue of synchronous and metachronous localizations of the disease, it is hypothesized that they are interconnected by "biological interactions" which determine and sustain the pathologic process. Based on the biological characteristics of an experimental model (the follicular center cell "lymphoma" of the SJL murine strain), it is suggested that these human "non-monomorphous" malignant diseases should be regarded as a continuous spectrum of lymphoproliferative disorders sustained by a biological loop which interconnects different cell populations able to stimulate each other for growth.
Human Neutrophil Elastase Responsive Delivery from Poly(ethylene glycol) Hydrogels (2009)

A novel enzyme-responsive hydrogel drug delivery system was developed with the potential to treat inflammation locally. Human neutrophil elastase (HNE) is a serine protease secreted by neutrophils which are the first cells recruited to inflammatory sites. We exploited this cell-secreted enzyme as a biological cue for controlled release. HNE sensitive peptide linkers were immobilized within poly(ethylene glycol) hydrogels using photopolymerization techniques. The kinetics of the enzyme reaction within the gel was tailored by varying the amino acid residues present in the P1 and P1' substrate positions (immediately adjacent to cleavage location). A novel FRET-based hydrogel platform was designed to characterize the accessibility of the substrate within the cross-linked, macroscopic hydrogel. Lastly, a diffusion-reaction mathematical model with Michaelis-Menten kinetics was developed to predict the overall release profile and captured the initial 80% of the experimentally observed release. The hydrogel platform presented shows highly controlled release kinetics with potential applications in cellular responsive drug delivery.
ML parameter estimation for Markov random fields with applications to Bayesian tomography (1998)

Markov random fields (MRF's) have been widely used to model images in Bayesian frameworks for image reconstruction and restoration. Typically, these MRF models have parameters that allow the prior model to be adjusted for best performance. However, optimal estimation of these parameters(sometimes referred to as hyper parameters) is difficult in practice for two reasons: i) direct parameter estimation for MRF's is known to be mathematically and numerically challenging; ii)parameters can not be directly estimated because the true image cross section is unavailable.In this paper, we propose a computationally efficient scheme to address both these difficulties for a general class of MRF models,and we derive specific methods of parameter estimation for the MRF model known as generalized Gaussian MRF (GGMRF).The first section of the paper derives methods of direct estimation of scale and shape parameters for a general continuously valued MRF. For the GGMRF case, we show that the ML estimate of the scale parameter, sigma, has a simple closed-form solution, and we present an efficient scheme for computing the ML estimate of the shape parameter, p, by an off-line numerical computation of the dependence of the partition function on p.The second section of the paper presents a fast algorithm for computing ML parameter estimates when the true image is unavailable. To do this, we use the expectation maximization(EM) algorithm. We develop a fast simulation method to replace the E-step, and a method to improve parameter estimates when the simulations are terminated prior to convergence.Experimental results indicate that our fast algorithms substantially reduce computation and result in good scale estimates for real tomographic data sets.
Evaluation of the In Vitro and In Vivo Antifungal Activity of APX001A/APX001 Against Candida auris (2017)

Candida auris, an emerging multidrug-resistant yeast, causes deadly invasive infections with high mortality. C. auris strains often show high MICs to fluconazole and amphotericin B, and some are resistant to all 3 major antifungal classes, limiting treatment options. We tested 16 C. auris strains from a wide geographical area (Germany, Japan, S. Korea, and India) against 10 antifungals including APX001A (APXA), an antifungal with a novel mechanism of action (inhibition of the Gwt1 fungal enzyme). The prodrug APX001 (APX) is in clinical development and its efficacy was evaluated in an immunocompromised murine model of disseminated C. auris. MICs were determined by CLSI M27-A3 method. Mice were immunocompromised for the study. Treatment was initiated 2 hours post challenge. IP treatment groups included a vehicle control, APX 78mg/kg (mpk) BID, 78mpk TID, and 104mpk BID, and anidulafungin (AFG) 10mpk BID. Survival was monitored for 16d post inoculation. Susceptibility. APXA had significantly lower MIC50 and MIC90 values (concentration that inhibits 50 and 90% of the tested isolates, respectively) than the other tested antifungals with a MIC90 of 0.031 µg/mL (Table 1). Survival. 100% mortality in the vehicle-treated control group occurred by 6d. Significant efficacy was observed in all APX treatment groups with 90, 100, and 80% survival observed respectively for APX 78 mpk BID; 78 mpk TID and 104 mpk BID. AFG treatment resulted in 50% survival at 16d. Mice in all of the APX treated groups had a significantly higher % survival compared with the AFG and vehicle groups. APXA was the most active antifungal agent in vitro. The prodrug APX resulted in significantly better survival than AFG in a C. auris disseminated infection model. Thus APX may be a viable treatment for C. auris infections. Table 1: Susceptibility of 16 C. auris isolates against antifungals K. J. Shaw, Amplyx Pharmaceuticals Inc.: Employee, Salary; M. Ghannoum, Amplyx Pharmaceuticals: Consultant, Research Contractor and Scientific Advisor, Consulting fee and Research grant; Cidara Therapeutics: Consultant and Research Contractor, Consulting fee and Research grant
Studies in Polyphenol Chemistry and Bioactivity. 2.1 Establishment of Interflavan Linkage Regio- and Stereochemistry by Oxidative Degradation of an O-Alkylated Derivative of Procyanidin B2 to (R)-(−)-2,4-Diphenylbutyric Acid (2000)

The assignment of interflavan bond regio- and stereochemistry in oligomeric proanthocyanidins has in the past relied on empirical spectroscopic techniques which are influenced by the conformation of the C rings. Only recently was the 4,8-regiochemistry of procyanidin B2 (3b) firmly established by 2-dimensional NMR methods. We describe herein the proof of 4beta-stereochemistry in 3b by oxidative degradation of the derivative 3d bearing differential (O-benzyl and O-methyl) protecting groups in its "top" and "bottom" epicatechin moieties, to (R)-(-)-2,4-diphenylbutyric acid. The key elements of the degradative process are (1) removal of the C-3 alcohol functions through a modified Barton deoxygenation employing hypophosphorous acid as the reducing agent; (2) deprotection of the "top" unit by hydrogenolysis, followed by exhaustive aryl triflate formation with N,N-bis(trifluoromethanesulfonyl)aniline and DBU in DMF; (3) hydrogenolytic deoxygenation of the "top" unit over Pearlman's catalyst with concomitant scission of the O-C2 bond; (4) selective oxidation of the "bottom" unit with NaIO4/RuCl3. The hitherto unreported absolute configuration of (-)-2,4-diphenylbutyric acid was established as R by X-ray crystal structure analysis of the (R)-(+)-alpha-methylbenzylamine salt. As a corollary, the selectivity of hydrogenolytic and solvolytic reactions of epicatechin-derived tetrasulfonates has been investigated.
Abstract P2-10-01: Validation that a histone gene signature predicts anthracycline response in early breast cancer (2018)

Abstract Background: The use of anthracycline-based chemotherapies has improved overall and disease free survival in breast cancer. However, anthracyclines can have significant toxicities including cardiotoxicity and leukemia. It is, therefore, imperative to identify those patients who will benefit from adjuvant anthracycline treatment and patients who could be spared unnecessary toxicities and be considered for alternative adjuvant therapy. Previous work performed by our laboratory identified a histone gene expression signature as a predictive marker of anthracycline benefit in the BR9601 clinical trial. In this study we validate the 18 histone gene signature in the MA.5 clinical trial and examine the role of the signature in individual intrinsic subtypes of breast cancer. Methods We analysed the CCTG MA.5 clinical trial in a prospectively planned retrospective biomarker approach to validate this signature and tested the role of intrinsic subtyping as predictive markers of anthracycline benefit. RNA was extracted from patients in the MA.5 adjuvant trial evaluating the addition of epirubicin (E) to CMF and analysed using NanoString technology. Log-rank analyses validated the predictive values of the signature on distant relapse-free survival (DRFS). Cox-regression models tested independent predictive value on DRFS in the presence of treatment, age, tumour size, nodal status, HER2, ER status and grade, and treatment by marker interactions. Results Analysis of the MA.5 clinical cohort revealed that patients whose tumour had low histone gene signature expression experienced increased DRFS (HR: 0.54, 95% CI 0.38-0.76, p=0.001) when treated with CEF compared with patients treated with CMF alone. Conversely, there was no apparent benefit of CEF vs CMF in patients with high histone gene expression signature (HR: 1.01, 95%CI 0.66-1.55, p=0.963). After multivariate analysis and adjustment for HER2, nodal status, age, grade and ER, the treatment by marker interaction for the gene signature was 0.54 (95%CI 0.31-0.94, p=0.030) for DRFS. The predictive impact of the histone signature was independent of intrinsic subtype. Conclusion The histone gene expression signature is an independent predictor of anthracycline benefit and could be a potential candidate diagnostic assay for patients with early breast cancer. Citation Format: Spears M, Kornaga E, Lyttle N, Liao L, Bayani J, Quintayo M-A, Yao CQ, D'Costa A, Boutros PC, Twelves CJ, Pritchard KI, Levine MN, Nielsen TO, Shepherd L, Bartlett JMS. Validation that a histone gene signature predicts anthracycline response in early breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-10-01.
Catalytically active and thermally stable core–shell gold–silica nanorods for CO oxidation (2021)

Deactivation based on sintering phenomena is one of the most costly issues for the industrial application of metal nanoparticle catalysts. To address this drawback, mesoporous silica encapsulation is reported as a promising strategy to stabilize metallic nanoparticles towards use in high temperature catalytic applications. These protective shells provide significant structural support to the nanoparticles, while the mesoporosity allows for efficient transport of the reactants to the catalytically active surface of the metallic nanoparticle in the core. Here, we extend the use of gold nanorods with mesoporous silica shells by investigating their stability in the CO oxidation reaction as an example of high temperature gas phase catalysis. Gold nanorods were chosen as the model system due to the availability of a simple, high yield synthesis method for both the metallic nanorods and the mesoporous silica shells. We demonstrate the catalytic activity of gold nanorods with mesoporous silica shells at temperatures up to 350 °C over several cycles, as well as the thermal stability up to 500 °C, and compare these results to surfactant-stabilized gold nanorods of similar size, which degrade, and lose most of their catalytic activity, before reaching 150 °C. These results show that the gold nanorods protected by the mesoporous silica shells have a significantly higher thermal stability than surfactant-stabilized gold nanorods and that the mesoporous silica shell allows for stable catalytic activity with little degradation at high temperatures.
Photochemical Flow Synthesis of 3‐Hydroxyazetidines (2019)

Abstract A photo‐flow Norrish–Yang cyclisation has been devised that delivers 3‐hydroxyazetidines in good yields. The high reproducibility and short residence times of the flow process enables easy scaling of the transformation allowing access to these valuable chemical entities at synthetically useful multi‐gram scales. A systematic exploration of the constituent structural components was undertaken allowing an understanding of the reactivity and functional group tolerance of the transformation.
Timely Updates With Priorities: Lexicographic Age Optimality (2022)

In this paper, we consider a scheduling problem, in which several streams of status update packets with different priority levels are sent through a shared channel to their destinations. We introduce a notion of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">lexicographic age optimality</i> , or simply <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">lex-age-optimality</i> , to evaluate the performance of multi-class status update policies. In particular, a lex-age-optimal scheduling policy first minimizes the Age of Information (AoI) metrics for high-priority streams, and then, within the set of optimal policies for high-priority streams, achieves the minimum AoI metrics for low-priority streams. We propose a new scheduling policy named Preemptive Priority, Maximum Age First, Last-Generated, First-Served (PP-MAF-LGFS), and prove that the PP-MAF-LGFS scheduling policy is lex-age-optimal. This result holds (i) for minimizing any time-dependent, symmetric, and non-decreasing age penalty function; (ii) for minimizing any non-decreasing functional of the stochastic process formed by the age penalty function; and (iii) for the cases where different priority classes have distinct arrival traffic patterns, age penalty functions, and age penalty functionals. For example, the PP-MAF-LGFS scheduling policy is lex-age-optimal for minimizing the probability of age violation of a high-priority stream and the time-average age of a low-priority stream. Numerical results are provided to illustrate our theoretical findings.
Antagonistic Actions of MIF-I on the Hypothermia and Hypomotility Induced by Beta-Endorphin Or Morphine (1980)

Recently it has been suggested that MIF-I can act as an opiate antagonist for analgesia. Therefore, rats kept at 4 degrees C were pretreated with MIF-I in an attempt to extend the observation to a nonanalgesic opiate effect by determining any blockade of the thermal response to beta-endorphin and morphine. MIF-I, at an ip dose of 1.0 mg/kg, was found to block the thermal responses to beta-endorphin injected ip at doses of 0.1 and 1.0 mg/kg. A lower dose (0.1 mg/kg, ip) of MIF-I, or naloxone (10 mg/kg), was also able to block the thermal effects of 30 and 60 mg/kg doses of morphine. However, an ip dose of 1.0 mg/kg MIF-I potentiated the hypothermic effects of morphine but, like naloxone, reduced the magnitude of the decrease in the level of motor activity induced by beta-endorphin or by morphine. The results of this study demonstrate a nonanalgesic situation in which MIF-I can act as an antagonist of opiate effects after peripheral injection.
Bacteriological evaluation of a new air turbine handpiece for preventing cross-contamination in dental procedures. (1994)

An autoclavable air turbine handpiece, Air Flushing Clean System (AFCS) (Osada Electric Co., Ltd., Tokyo, Japan) was developed for use in dentistry with the objective of reducing cross-contamination. Its potential for bacterial contamination was investigated in vitro using two bacterial strains (Streptococcus mutants ATCC 25175 and Staphylococcus aureus FDA 209 P). In theory, this device should prevent cross-contamination of the internal water and air lines of the handpiece, by maintaining an internal positive pressure even after the turbine is stopped. In the present study, this AFCS device was found to reduce the bacterial contamination within the air turbine handpiece more effectively than the conventional handpiece used according to accepted protocol. The reduction of such contamination by the AFCS is in keeping with the recent objective of the American Dental Association to reduce cross-contamination during dental procedures.
New analytical models and probability density functions for fading in wireless communications (2002)

This paper presents new envelope probability density functions (PDFs) that describe small-scale, local area fading experienced by narrow-band wireless receivers. The paper also develops novel PDFs that describe the local area fading of two specular multipath components in the presence of other diffusely propagating waves. These PDFs are studied in the context of classical fading PDFs such as the Rayleigh, Rician, and other distributions.
The need for a digital rights management framework for the next generation of e-government services (2004)

The amount of government information is huge and relies mostly on traditional systems, inaccessible to citizens and often to government departments. In today's digital era, most of this content can be more intelligently processed and integrated within e-government. In the world of the future, where ambient intelligence and e-governments are a reality, citizens will interact with the available services in all areas of their lives; a situation that presents new challenges in the area of Digital Rights Management (DRM). Taking into account the nature of the information and the needs of different governmental departments and citizens, any e-government research must give full attention to DRM. In the process towards successful e-government, properly handling privacy, security and trust is an indispensable precondition for reliable legal safeguards, reliable technology and secure business, and for achieving acceptance by citizens. Therefore, we propose to establish a Network of Excellence (NoE) for a framework for policy, privacy, security, trust and risk management for DRM. The NoE will consist of experts from various disciplines and will conduct and guide on-going and future high quality research on e-government related domains.
Aluminum-Containing Phases in Tank Waste: Precipitation and Deposition of Aluminum-Containing Phases (2006)

Aluminosilicate deposit buildup experienced during the tank waste volume-reduction process at the Savannah River Site (SRS) required an evaporator to be shut down in October 1999. Recent investigations illustrated the accumulation 7 wt% uranium, 3% was 235U and absent of neutron poisons, within these deposits and presented a criticality concern. The Waste Processing Technology Section of Westinghouse Savannah River Company at SRS is now collaborating with a team from Pacific Northwest National Laboratory in efforts to identify the phases controlling uranium solubility and understand the conditions under which they precipitate.
Overriding Standard Decoding: Implications of Recoding for Ribosome Function and Enrichment of Gene Expression (2001)

When the genetic code and the general mechanism ofits readout were elucidated, there was no reason to thinkthat decoding would not be uniform—that the code wouldbe read differently at specific sites within coding sequences. However, we now know that ribosomes showremarkable versatility in response to recoding signals.They can shift reading frame in either direction, bypassblocks of nucleotides within mRNA or redefine themeaning of certain codons, usually stop codons. The crucial signals can involve not only specific sequences in themRNA, but also mRNA structures, specialized translation factors, specialized tRNAs, and even amino acid sequences in the nascent peptide chain...
SOFTWARE RELIABILITY ESTIMATIONS THROUGH USAGE ANALYSIS OF SPECIFICATIONS AND DESIGNS (1996)

This paper presents a method proposal for estimation of software reliability before the implementation phase. The method is based upon that a formal specification technique is used and that it is possible to develop a tool performing dynamic analysis, i.e., locating semantic faults in the design. The analysis is performed with both applying a usage profile as input as well as doing a full analysis, i.e., locate all faults that the tool can find. The tool must provide failure data in terms of time since the last failure was detected. The mapping of the dynamic failures to the failures encountered during statistical usage testing and operation is discussed. The method can be applied either on the software specification or as a step in the development process by applying it on the software design. The proposed method allows for software reliability estimations that can be used both as a quality indicator, and for planning and controlling resources, development times, etc. at an early stage in the development of software systems.
An adaptive digital controller for a unity power factor converter (1996)

This paper describes an adaptive digital controller for a unity power factor AC-DC power converter. The controller is based on a linear large-signal model of the boost power converter. A hardware design is presented and analyzed, followed by the software implementation of the control algorithm. Issues in digital control of power converters, such as quantization effects and fixed-point representation of system parameters, are examined in the context of this system. Experimental results are presented and compared with simulations.
Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples (2021)

Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against nasopharyngeal swab specimens and found saliva methods require further optimization to match this gold standard. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.