gebhart/patrepeval huggingface dataset:
Protein Release in Recombinant Escherichia coli Using Bacteriocin Release Protein (1992)

The effect of induction level of the bacteriocin release protein (BRP) on cell growth characteristics, protein expression, and protein release in a recombinant strain of Escherichia coli RR1 was investigated. Mitomycin C, the inducing agent, when added to the growth medium in moderate amounts (up to 200 ng/mL) was observed to enhance the release of periplasmic proteins from the cell to the fermentation broth substantially. The percentages of release of the proteins alpha-amylase and beta-lactamase were increased by factors of about 7 and 3, respectively, upon induction of the BRP. The percentage of alpha-amylase released into the broth increased from only about 5% to almost 50% with the aid of BRP. The cell growth curve and low extracellular activity of the cytoplasmic protein beta-galactosidase were indicative that cell lysis did not occur in an appreciable amount at a low induction level, with a mitomycin C concentration of less than 300 ng/mL.
Photochemical Route to the Synthesis of Thiolane 1-Oxides (2006)

The preparation of thiolane 1-oxide 10 by photochemically mediated rearrangement of sulfoxide 9 in high yield is described. The efficient construction of quaternary carbon centers underscores the utility of this methodology in organic synthesis. Further manipulation of photoadduct 10 leads to the formation of diverse heterocyclic structures.
Effect of degree of crystallinity on charge transport in ferroelectric semicrystalline polymer film (2015)

This paper describes 3D particle-in-cell (PIC) simulation of charge injection and transport through ferroelectric semicrystalline polymer (e.g. PVDF) film comprised of nanocrystallites in an amorphous matrix with varying degrees of crystallinity. The classical electrical double layer (EDL) model for a monopolar core is extended (eEDL) to represent the nanocrystallite by replacing it with a dipolar core. Charge injection at the electrodes assumes metal-polymer Schottky emission at low to moderate fields and Fowler-Nordheim tunneling at high fields. Injected particles propagate via field-dependent Poole-Frenkel mobility. In the eEDL model, the initial attachment of charge particles forms the bound Stern-Helmholtz layer leading to Maxwell-Wagner-Sillars polarization. Subsequent waves of charge particles are repelled by the attached charge resulting in the diffuse Gouy- Chapman transport layer. The simulation algorithm uses a boundary integral equation method (BIEM) for solution of the Poisson equation coupled with a second-order predictor-corrector scheme for robust time integration of the equations of motion. The stability criterion of the explicit algorithm conforms to the Courant-Friedrichs-Levy (CFL) limit assuring robust and rapid convergence. The model is capable of simulating a wide dynamic range spanning leakage current to pre-breakdown levels. Simulation results for semicrystalline film with varying degrees of crystallinity indicate that charge transport behavior depends on nanoparticle polarization with anti-parallel orientation showing the highest conduction and therefore lowest level of charge trapping in the interaction zone. Charge attachment to nanocrystallites increase with vol% loading or degree of crystallinity, and saturates at 40 vol% for the set of simulation parameters. The eEDL model predicts the intuitive meandering pathways of charge particle trajectories, which get progressively more inclined from normal incidence with increasing vol% loading.
13 C-Labeled Gluconate Tracing as a Direct and Accurate Method for Determining the Pentose Phosphate Pathway Split Ratio in Penicillium chrysogenum (2006)

In this study we developed a new method for accurately determining the pentose phosphate pathway (PPP) split ratio, an important metabolic parameter in the primary metabolism of a cell. This method is based on simultaneous feeding of unlabeled glucose and trace amounts of [U-13C]gluconate, followed by measurement of the mass isotopomers of the intracellular metabolites surrounding the 6-phosphogluconate node. The gluconate tracer method was used with a penicillin G-producing chemostat culture of the filamentous fungus Penicillium chrysogenum. For comparison, a 13C-labeling-based metabolic flux analysis (MFA) was performed for glycolysis and the PPP of P. chrysogenum. For the first time mass isotopomer measurements of 13C-labeled primary metabolites are reported for P. chrysogenum and used for a 13C-based MFA. Estimation of the PPP split ratio of P. chrysogenum at a growth rate of 0.02 h(-1) yielded comparable values for the gluconate tracer method and the 13C-based MFA method, 51.8% and 51.1%, respectively. A sensitivity analysis of the estimated PPP split ratios showed that the 95% confidence interval was almost threefold smaller for the gluconate tracer method than for the 13C-based MFA method (40.0 to 63.5% and 46.0 to 56.5%, respectively). From these results we concluded that the gluconate tracer method permits accurate determination of the PPP split ratio but provides no information about the remaining cellular metabolism, while the 13C-based MFA method permits estimation of multiple fluxes but provides a less accurate estimate of the PPP split ratio.
Non-diffracting broadband incoherent space–time fields (2019)

Space-time (ST) wave packets are coherent pulsed beams that propagate diffraction-free and dispersion-free by virtue of tight correlations introduced between their spatial and temporal spectral degrees of freedom. Less is known of the behavior of incoherent ST fields that maintain the spatio-temporal spectral structure of their coherent wave-packet counterparts while losing all purely spatial or temporal coherence. We show here that structuring the spatio-temporal spectrum of an incoherent field produces broadband incoherent ST fields that are diffraction-free. The intensity profile of these fields consists of a narrow spatial feature atop a constant background. Spatio-temporal spectral engineering allows controlling the width of this spatial feature, tuning it from a bright to a dark diffraction-free feature, and varying its amplitude relative to the background. These results pave the way to new opportunities in the experimental investigation of optical coherence of fields jointly structured in space and time by exploiting the techniques usually associated with ultrafast optics.
Early Responses in Patient-reported Outcomes Are Predictors for Mucosal Healing in Patients with Moderately to Severely Active Ulcerative Colitis Treated with Golimumab: Results from PURSUIT SC Induction (2013)

Purpose: To assess for an association of patient-reported stool frequency and rectal bleeding with mucosal healing (MH) based on endoscopy in patients with active ulcerative (UC). Methods: Patients with active UC defined by a Mayo score of 6-12, including an endoscopy subscore of ≥2, were randomized to placebo (PBO)/PBO, GLM 200 mg/100 mg, GLM 400 mg/200 mg, at weeks 0 and 2. Patient-reported stool frequency and rectal bleeding from weeks 0-6 were collected from the most recent consecutive 3-day period within the 2 weeks prior to a visit. A responder was defined as normalized stool frequency or no rectal bleeding. MH was defined as an endoscopy subscore of the Mayo score of 0 or 1. Odds ratio (OR), positive predictive value (PPV), and likelihood ratio positive (LR+) were estimated for predicting MH, using normalized stool frequency or no rectal bleeding. Results: A high proportion of patients reported abnormal stool frequency (99%) and rectal bleeding (86.9%) at week 0. In these post-hoc analyses, significant differences in stool frequency and rectal bleeding were observed between treatment groups as early as week 2 (all nominal p-values<0.001) (Table). At week 6, a greater proportion of patients in the pooled GLM group vs. PBO reported normalized stool frequency (17.7%, vs 7.0%) or no rectal bleeding (52.8% vs. 34.0%) (all nominal p-values<0.001). Among patients who reported no rectal bleeding consistently from week 2-6, 66.4% achieved MH at week 6, compared to 13.2% of patients with rectal bleeding through week 6 (OR 13.0, nominal p<0.001, PPV=0.66, LR=3.7). Similarly, among patients with normalized stool frequency consistently from week 2 through wk 6, 78.3% achieved mucosal healing at week 6 vs. 30.2% of patients with abnormal stool frequency through week 6 (OR=8.3, nominal p<0.001, PPV=0.78, LR=7.1).Table: Table. Post-hoc analysis of stool frequency and rectal bleeding scoreConclusion: Treatment with SC GLM led to early improvement in patient-reported outcomes of stool frequency and rectal bleeding. The normalization of stool frequency and improvement in rectal bleeding associated with MH at week 6 in patients with UC. Disclosure - William J Sandborn, Walter Reinisch, Brian G. Feagan, Peter Gibson, Judith Collins, Gunnar Jarnerot, Paul Rutgeerts, Jean-Frederic Colombel-All Grant/Research Support: Janssen Research and Development, LLC; Colleen Marano, Richard Strauss, Jewel Johanns, and Hongyan Zhang-All employees: Janssen Research and Development, LLC; Chenglong Han-Employee: Janssen Global Services, LLC. This research was supported by an industry grant from Janssen Research and Development, LLC.
Towards the Resilience Assessment of Electric Distribution System to Earthquakes and Adverse Meteorological Conditions (2018)

The paper provides, as a first step, a critical, although not-exhaustive, review of the steps required for assessing the resilience of electric distribution systems to natural hazards, and identifies the required metrics and models still to be defined. Aiming to contribute towards that, the paper proposes an empirical-based analytical formula for estimating the expected damage frequencies to underground cable joints, when subjected to overheating. Empirical-based formulas for estimating the damage frequency to underground cables, subjected to earthquakes are also reported in the paper. The implementation of such models within a Decision Support System able to support resilience enhancement decision making processes is briefly illustrated in the paper.
Endocrine Disrupting Effects of Herbicides and Pentachlorophenol: In Vitro and in Vivo Evidence (2009)

The potential for agricultural chemicals to cause endocrine disruption (ED) in humans and wildlife is an increasing concern; however, the effects of commonly used pesticides at environmentally relevant concentrations are largely unknown. Therefore, 12 environmentally relevant pesticides (11 herbicides and pentachlorophenol (PCP)) were tested for their endocrine disrupting potential in two in vitro assays. A recombinant yeast screen was used to detect receptor mediated (anti-) estrogenic and (anti-) androgenic activity (concentration range: 0.01-1000 microM), and cultured Xenopus oocytes were used to measure effects on the ovulatory response and ovarian steroidogenesis (concentration range: 0.00625-62.5 microM). Eleven pesticides were active in at least one assay (isoproturon, diuron, linuron, 4-chloro-2-methylphenoxy acetic acid (MCPA), mecoprop, atrazine, simazine, PCP, trifluralin, chlorpropham, bentazone), and one had no effect (2,4-dichlorophenoxy acetic acid (2,4,-D)). The most common effects were antiestrogenic/ antiandrogenic activity in the yeast screen, and inhibition of ovulation in vitro, accompanied by decreased testosterone production. Estrogenic activity was never observed. In addition, the most potent compound identified in vitro (PCP) was tested for ED activity in vivo. A short-term exposure (6 days) of adult female Xenopus to low concentrations (0.1 or 1 microg/L; 0.375 or 3.75 nM) resulted in minor alterations in plasma hormone levels and toxic effects on the ovary. Changes in in vitro human chorionic gonadotropin (hCG) stimulated hormone production in ovarian follicles from exposed individuals was also observed. In conclusion, novel effects of herbicides and PCP at environmentally relevant concentrations were found, and the effects of these compounds on humans and/or wildlife warrant further investigation.
The BLUE active queue management algorithms (2002)

In order to stem the increasing packet loss rates caused by an exponential increase in network traffic, the IETF has been considering the deployment of active queue management techniques such as RED (random early detection) (see Floyd, S. and Jacobson, V., IEEE/ACM Trans. Networking, vol.1, p.397-413, 1993). While active queue management can potentially reduce packet loss rates in the Internet, we show that current techniques are ineffective in preventing high loss rates. The inherent problem with these algorithms is that they use queue lengths as the indicator of the severity of congestion. In light of this observation, a fundamentally different active queue management algorithm, called BLUE, is proposed, implemented and evaluated. BLUE uses packet loss and link idle events to manage congestion. Using both simulation and controlled experiments, BLUE is shown to perform significantly better than RED, both in terms of packet loss rates and buffer size requirements in the network. As an extension to BLUE, a novel technique based on Bloom filters (see Bloom, B., Commun. ACM, vol.13, no.7, p.422-6, 1970) is described for enforcing fairness among a large number of flows. In particular, we propose and evaluate stochastic fair BLUE (SFB), a queue management algorithm which can identify and rate-limit nonresponsive flows using a very small amount of state information.
Animal Population Estimation Using Flickr Images (2017)

While the technologies of the Information Age have produced staggering amounts of data about people, they are by and large failing the world’s wildlife. Even the simplest and most critical piece of information, the number of animals of a species, is either unknown or is uncertain for most species. Here, we propose to use images of wildlife posted on social media platforms, together with animal recognitions software and mark-recapture models, to estimate population sizes. We show that population size estimates from social media photographs of animals can produce robust results, yet more work is needed to understand biases inherent in the approach.
Vision Threatening Disease Triage Using Tele-Ophthalmology during COVID-19 in the Emergency Department: A Pilot Study (2021)

Purpose : The Centers for Disease Control reports 28.2% of surveyed US adults had reduced access to medical care (June/August 2020) due to the COVID-19 pandemic, with 8.9% reporting reduced access to vision care. A non-mydriatic digital retinal camera was piloted for deployment to the Emergency Department (ED) to help address this gap in vision care. Referrals for clinical follow-up in vision threatening diseases (VTDs) such as age-related macular degeneration, cataracts, diabetic retinopathy (DR), and glaucoma were assessed with human readers. Artificial Intelligence (AI) deep learning software was evaluated in known DR cases. Methods : 33 patients with known VTDs (48.48% male, avg 59.33 years) and 36 control subjects (41.67% male, avg 31.33 years) were included in tele-ophthalmology screening. A Canon CR-2 Plus AF non-mydriatic retinal camera captured 45-degree angle color and auto-fluorescence images of the eyes. Images (136 eyes) were graded by a certified telemedicine reader on site and an off-site clinical ophthalmologist following International Clinical Diabetic Retinopathy Disease Severity Scale (ICDRSS). Intergrader agreement between readers was evaluated with Cohen's kappa. An automated deep learning screening software optimized for DR (SELENA+, EyRIS Pte Ltd, Singapore) performed independent validation of readable color fundus images (17 eyes). Results : 5.07% of images were deemed unreadable by graders due to poor quality. Intergrader agreement for subject referral was κ = 0.710 (95% CI 0.545-0.875, p<.0005), with the clinical ophthalmologist generating more referrals than the telemedicine reader. Readers had 96.97% sensitivity (95% CI 91.12-1.028) and 72.22% specificity (95% CI 57.59- 86.85) in detecting referable disease. Positive predictive value was 76.19% (CI 63.31%- 89.07%) and negative predictive value was 96.30% (CI 89.17%- 1.034%). Of the 10 false positives, 6 were referred for rule out of glaucoma. Four had early stage cataracts that were deemed nonurgent. SELENA+ referred 100% of the known 9 DR patients. Conclusions : Tele-ophthalmology deployment in the ED helps limit patient and staff exposure to SARS-CoV-2 without sacrificing evaluation for VTDs. Tele-ophthalmology readers err on the side of caution to avoid missing VTD in a given patient. Use of AI can help keep strict adherence to referral guidelines.
Modeling and analysis of proximity losses in high-speed surface permanent magnet machines with concentrated windings (2010)

Surface permanent magnet (SPM) machines can be designed with fractional slot-concentrated windings (FSCW) to achieve extended speed ranges. High-speed operation can lead to significant levels of proximity losses in the stator windings due to substantial spatial harmonic magnetic fields in the air-gap as well as the high-frequency currents themselves. An integrated analysis tool is presented in this paper to calculate the strand- and bundle-level proximity losses in slotted stator conductors without requiring finite element analysis. A combination of analysis techniques, including Laplace equation solutions and conformal mapping, is used to estimate the magnetic field in each stator slot, providing the basis for proximity loss estimation. The match between losses estimated using the analytical model and finite element analysis is very promising.
Pim Kinase Substrate Identification and Specificity (2006)

The Pim family of Ser/Thr kinases has been implicated in the process of lymphomagenesis and cell survival. Known substrates of Pim kinases are few and poorly characterized. In this study we set out to identify novel Pim-2 substrates using the Kinase Substrate Tracking and Elucidation (KESTREL) approach. Two potential substrates, eukaryotic initiation factor 4B (eIF4B) and apoptosis inhibitor 5 (API-5), were identified from rat thymus extracts. Sequence comparison of the Pim-2 kinase phosphorylation sites of eIF4B and mouse BAD, the only other known Pim-2 substrate, revealed conserved amino acids preceding the phosphorylated serine residue. Stepwise replacement of the conserved residues produced a consensus sequence for Pim kinase recognition: RXRHXS. Pim-1 and Pim-2 catalyzed the phosphorylation of this recognition sequence 20-fold more efficiently than the original (K/R-K/R-R-K/R-L-S/T-a; a = small chain amino acid) Pim-1 phosphorylation site. The identification of the novel Pim kinase consensus sequence provides a more sensitive and versatile peptide based assay for screening modulators of Pim kinase activity.
Abstract P321: Clozapine-induced Hypertension: Role of the Dopamine Type 4 Receptor (D4R) in Human Renal Proximal Tubule Cells (RPTC) (2017)

Clozapine (CLZ), a potent D 4 R antagonist that is an effective antipsychotic drug for the treatment of schizophrenia, is associated with hypertension. The hypertensive side effect of CLZ may be through inhibition of the D 4 R because germline deletion of D 4 R in mice causes hypertension. The hypertension caused by germline deletion of D 4 R may, in part, be due to increased renal expression of the angiotensin type 1 receptor (AT 1 R) and renal expression of sodium exchangers, transporters, and pumps, e.g., NHE3, NKCC2, NCC, and Na + K + /ATPase, α subunit. CLZ administered subcutaneously (20mg/kg/day/x3 days, n=5) in mice induced hypertension, shifted the pressure-natriuresis plot to the right, and increased the renal expressions of NCC and Na + K + /ATPase, α subunit, relative to vehicle-treated mice (n=5). Activation of D 4 R decreased AT 1 R expression and Na + K + /ATPase activity in rat renal proximal tubule cells (RPTCs). Therefore, we studied two groups: subjects 18 to 75 years old with a DSM-IV diagnosis of schizophrenia or schizoaffective disorder treated with CLZ for &gt;2 months (CLZ, N=32) and untreated healthy controls ( HC , N=20) without psychiatric illness. There were no significant differences in blood pressure (BP) between the two groups since more than half of the CLZ participants received antihypertensive medication. We studied RPTCs cultured from the participant’s urine (CLZ, N=18; HC, N=9) and treated those cells with 100 nM CLZ. CLZ decreased D 4 R expression in both HC and CLZ groups ( HC , VEH 1.04±0.17 vs CLZ 0.73±0.09, n=9, paired t-test, P&lt;0.05; CLZ, VEH 1.02±0.09 vs CLZ 0.75±0.06, n=16, paired t-test, P&lt;0.01). CLZ also increased reactive oxygen species (Rosstar550 assay) in the HC but not CLZ-treated group ( HC , VEH 0.92±0.07 vs CLZ 1.02±0.09, n=8, paired t-test , P&lt;0.05; CLZ VEH 1.09±0.18 vs CLZ 1.07±0.18, n=14). The density of plasma membrane AT 1 R tended to be higher in CLZ-treated hypertensive (CLX HP) than the CLZ-treated normotensive participants (CLZ NP): ( HC , 0.28±0.08 n=8; CLZ NP, 0.10±0.02 n=4; CLZ HP, 0.81±0.31 n=7). Thus, CLZ may induce hypertension through a D 4 R/AT 1 R-mediated mechanism similar to that reported in D 4 R knockout mice. Additional studies will determine if CLZ increases sodium transport in human RPTCs.
Nano-scale 3-D Characterization of Materials Using FIB-SEM (2006)

Extended abstract of a paper presented at Microscopy and Microanalysis 2006 in Chicago, Illinois, USA, July 30 – August 3, 2005
Oral squamous cell carcinoma diagnosed from saliva metabolic profiling (2020)

Saliva is a noninvasive biofluid that can contain metabolite signatures of oral squamous cell carcinoma (OSCC). Conductive polymer spray ionization mass spectrometry (CPSI-MS) is employed to record a wide range of metabolite species within a few seconds, making this technique appealing as a point-of-care method for the early detection of OSCC. Saliva samples from 373 volunteers, 124 who are healthy, 124 who have premalignant lesions, and 125 who are OSCC patients, were collected for discovering and validating dysregulated metabolites and determining altered metabolic pathways. Metabolite markers were reconfirmed at the primary tissue level by desorption electrospray ionization MS imaging (DESI-MSI), demonstrating the reliability of diagnoses based on saliva metabolomics. With the aid of machine learning (ML), OSCC and premalignant lesions can be distinguished from the normal physical condition in real time with an accuracy of 86.7%, on a person by person basis. These results suggest that the combination of CPSI-MS and ML is a feasible tool for accurate, automated diagnosis of OSCC in clinical practice.
A 65-nm CMOS Temperature-Compensated Mobility-Based Frequency Reference for Wireless Sensor Networks (2011)

A temperature-compensated CMOS frequency reference based on the electron mobility in a MOS transistor is presented. Over the temperature range from -55°C to 125°C , the frequency spread of the complete reference is less than ±0.5% after a two-point trim and less than ±2.7% after a one-point trim. These results make it suitable for use in Wireless Sensor Network nodes. Fabricated in a baseline 65-nm CMOS process, the 150 kHz frequency reference occupies 0.2 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and draws 42.6 μA from a 1.2-V supply at room temperature.
Carbohydrate‐Based Antifungal Vaccines (2008)

This chapter contains sections titled: Introduction Terminology Antifungal Glycoconjugate Vaccines Antifungal Vaccines and the Immune System Summary Acknowledgment References
A Brief Overview of Research Into Radiation Source Development and Radiation Sensors in the Microfabrication Program at Sandia National Laboratories. (2012)

Abstract not provided.