gebhart/patrepeval huggingface dataset:
Protective Immunity to Malaria and Anti‐Erythrocyte Autoimmunity (1983)

The intraerythrocytic development of malaria parasites results in considerable modification and destruction of erythrocytes. This may lead to the breaking of tolerance such that immune recognition of 'self' or 'modified self' erythrocyte antigens by B or T lymphocytes occurs. Such recognition may be a vital factor in the induction of protective immunity even though it may also cause immunopathology. Serological and immunocytochemical assays have been used to demonstrate, in the serum of Plasmodium berghei-infected or immune rats, antibodies to isoantigenic determinants on infected erythrocytes. Absorption studies indicated that antigens specifically associated with parasitized erythrocytes and erythrocyte isoantigens were closely associated at the surface membrane. Extensive erythrocyte modification and destruction, artificially generated by phenylhydrazine treatment, significantly enhanced immunity against rodent malaria. In contrast, the generation of an incomplete anti-erythrocyte autoantibody response in mice by the injection of cross-reacting rat erythrocytes failed to augment protective responses to P. chabaudi. The reinjection of rat erythrocytes into mice previously injected with rat erythrocytes suppresses further autoantibody synthesis and the mice revert to the normal (Coombs-negative) state. Spleen cells from rat erythrocyte-treated mice transfer this suppression when injected into syngeneic recipients. Coombs-negative mice reinjected with rat erythrocytes failed to show enhanced protective responses to P. chabaudi. Spleen cells from such Coombs-negative mice, injected into sublethally irradiated recipients, increased the protective effects of concurrently transferred spleen cells from malaria-immune donors when the recipients were challenged with P. chabaudi.
Clinical <i>BRCA1/2</i> Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance (2020)

Reversion mutations in <i>BRCA1</i> or <i>BRCA2</i> are associated with resistance to PARP inhibitors and platinum. To better understand the nature of these mutations, we collated, codified, and analyzed more than 300 reversions. This identified reversion "hotspots" and "deserts" in regions encoding the <i>N</i> and <i>C</i> terminus, respectively, of BRCA2, suggesting that pathogenic mutations in these regions may be at higher or lower risk of reversion. Missense and splice-site pathogenic mutations in <i>BRCA1/2</i> also appeared less likely to revert than truncating mutations. Most reversions were <100 bp deletions. Although many deletions exhibited microhomology, this was not universal, suggesting that multiple DNA-repair processes cause reversion. Finally, we found that many reversions were predicted to encode immunogenic neopeptides, suggesting a route to the treatment of reverted disease. As well as providing a freely available database for the collation of future reversion cases, these observations have implications for how drug resistance might be managed in <i>BRCA</i>-mutant cancers. SIGNIFICANCE: Reversion mutations in <i>BRCA</i> genes are a major cause of clinical platinum and PARP inhibitor resistance. This analysis of all reported clinical reversions suggests that the position of <i>BRCA2</i> mutations affects the risk of reversion. Many reversions are also predicted to encode tumor neoantigens, providing a potential route to targeting resistance.<i>This article is highlighted in the In This Issue feature, p. 1426</i>.
Modern brachytherapy for localized prostate cancers: the northwest hospital (Seattle) experience. (2001)

Modern ultrasound-guided prostate brachytherapy is rapidly changing the way localized prostate cancer is managed. With routine use of prostate-specific antigen screening, prostate cancer is being diagnosed in younger men, who are understandably concerned about the morbidity of radical treatments that may significantly decrease their quality of life. Numerous studies of prostate brachytherapy have shown the excellent disease control rates achieved while maintaining low levels of urinary and erectile difficulties. This report examines a modern implant method of brachytherapy; describes patient selection for brachytherapy, alone and in combination with external beam therapy; and presents results from a series of men followed for 12 years.
Virus penetration of examination gloves. (1990)

Examination gloves worn for protection from biohazards were sampled and evaluated for their ability to exclude virus particles. We found that thin gloves manufactured from polyethylene or polyvinyl chloride are ineffective barriers while gloves of thin latex are superior but not without failure. Polyethylene and polyvinyl chloride gloves had failure rates of 40% and 22%, respectively. Following exposure to the common disinfectant, 70% ethanol, these failure rates increased to 94% and 56% for polyethylene and polyvinyl chloride gloves, respectively. Latex, although permeable to ethanol, was penetrated by virus less than 1% of the time regardless of whether the latex had been pre-exposed to disinfectant or not. This study highlights the need for caution on the part of those who rely upon examination gloves for protection from infectious agents as well as the need for establishing more adequate standards and testing procedures for their manufacture.
Easily Implementable Inventory Control Policies (1997)

This work was initiated and supported by a manufacturer of mail processing equipment, which stocks 30,000 distinct parts in a distribution center to support field maintenance of their equipment. To find an effective stocking policy for this system we formulate a constrained optimization model with the objective of minimizing overall inventory investment at the distribution center subject to constraints on customer service and order frequency. Because size, integrality, and nonconvexity make this problem intractable to exact analysis, we develop three heuristic algorithms based on simplified representations of the inventory and service expressions. These lead to what we call easily implementable inventory policies, in which the control parameters for a newly introduced part can be computed in closed form without reoptimizing the rest of the system. Numerical comparisons against a lower bound on the cost function show that even our simplest heuristic works well when a high service level is required. However, we show that a more sophisticated heuristic is more robustly accurate. We also compare our heuristics to methods previously in use by the firm whose system motivated this research and show that they are more efficient in the sense of attaining the same customer service level with a 20–25% smaller inventory investment. Finally, we discuss implementation issues related to the specific needs of the client firm, such as how to handle parts with no or low recent usage and dynamically changing demand for parts.
Construction of a fol mutant strain of Escherichia coli for use in dihydrofolate reductase mutagenesis experiments (1988)

A strain of Escherichia coli with the fol gene deleted and a kan gene inserted in its place was created for use in cloning and isolation of mutant dihydrofolate reductase. Southern blot analysis and dihydrofolate reductase enzyme assays confirmed the delta fol::kan genotype. A thyA mutation accompanied the fol deletion and is required for survival of a dihydrofolate reductase-deficient strain.
Propagation length of surface plasmons in a metal film with roughness (2009)

The propagation of laser-excited surface plasmons along a gold film with surface roughness is directly observed via scattered light. The attenuation length of surface plasmons in a broad wavelength interval is calculated for smooth gold and silver films. The surface roughness, which was characterized with an AFM, introduces corrections to the attenuation length, angular dependence of the surface plasmon resonance, and the effective dielectric constant of the metal film. These corrections are also taken into account and discussed.
Structure of the <i>Escherichia coli</i> RNA Polymerase α Subunit Amino-Terminal Domain (1998)

The 2.5 angstrom resolution x-ray crystal structure of the Escherichia coli RNA polymerase (RNAP) alpha subunit amino-terminal domain (alphaNTD), which is necessary and sufficient to dimerize and assemble the other RNAP subunits into a transcriptionally active enzyme and contains all of the sequence elements conserved among eukaryotic alpha homologs, has been determined. The alphaNTD monomer comprises two distinct, flexibly linked domains, only one of which participates in the dimer interface. In the alphaNTD dimer, a pair of helices from one monomer interact with the cognate helices of the other to form an extensive hydrophobic core. All of the determinants for interactions with the other RNAP subunits lie on one face of the alphaNTD dimer. Sequence alignments, combined with secondary-structure predictions, support proposals that a heterodimer of the eukaryotic RNAP subunits related to Saccharomyces cerevisiae Rpb3 and Rpb11 plays the role of the alphaNTD dimer in prokaryotic RNAP.
Gender Bias in Coreference Resolution (2018)

Rachel Rudinger, Jason Naradowsky, Brian Leonard, Benjamin Van Durme. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 2 (Short Papers). 2018.
<title>Micromachined electron gun array (MEGA)</title> (1995)

We present the Micro-machined Electron Gun Array (MEGA) as a massively-parallel approach to high throughput production electron beam lithography. The fabrication of the various components of the MEGA are described and the electron optical properties of micro- machined electron guns (MEGs) are studied using electron-optical simulation software. Electron-electron interaction between multiple beams is studied through Monte Carlo simulations for a number of configurations.
Ictal ECG changes in temporal lobe epilepsy (1995)

Changes in cardiac rhythm may occur during epileptic seizures and this has been suggested as a possible mechanism for sudden unexpected death amongst patients with chronic epilepsy (SUDEP). We have studied ECG changes during 61 complex partial seizures of temporal lobe origin in 20 patients. Tachycardia was observed in 24/61 (39%) and bradycardia in 3/61 (5%). The mean and median tachycardia rate was 139 and 140 beats/min (range 120-180). The longest R-R interval observed was 9 seconds. No difference was found in regard to the lateralisation of seizures and cardiac arrhytmia. One of the patients with bradycardia was fitted with a demand cardiac pacemaker, which appeared to decrease the number of his falls. In conclusion, ictal cardiac changes which may be seen in temporal lobe epilepsy (TLE) are sinus tachycardia and occasionally sinus bradycardia. Patients presenting vague complains suggestive of either TLE or cardiac dysrhythmia, simultaneous monitoring with EEG/ECG is required, and if the episodes are frequent, video-EEG should be considered. Further studies on this subject are warranted as this may shed some light on possible mechanisms for SUDEP.
Major Advances in Our Understanding of Nutritional Influences on Bovine Health (2006)

The Journal of Dairy Science has increasingly become a primary outlet for scientific research concerning the health of the dairy cow and her calf. This paper attempts to highlight Journal of Dairy Science articles that have linked nutrition and nutritional strategies to reduce disease incidence on the dairy farm. Disorders associated with an animal's inability to cope with the demands of high production include diseases such as milk fever and ketosis, which clearly are related to the cow's inability to maintain bodily functions in the face of negative calcium or energy balance. Improved nutrition of the late gestation cow can reduce the incidence of some of these disorders. Susceptibility to infectious disease is dependent on the integrity of the immune system, and recent studies have shed light on nutritional factors that affect leukocyte function. Other disorders, such as retained fetal membranes, udder edema, and displacement of the abomasum are not easily categorized as to their cause, but nutritional strategies have been developed to help prevent these disorders as well.
Transmission Power Control Techniques for MAC Protocols in Wireless Sensor Networks (2008)

Communication is usually the most energy-consuming event in wireless sensor networks (WSNs). The lifetime of these networks is determined by the capacity of batteries and one of the biggest challenges is to reduce the energy consumed in the communication. Several techniques to reduce the energy consumption have been proposed in routing protocols: diminish the traffic of data, optimize the routes or the control of the topology. However, the management and operation of the node’s radio is responsibility of the medium access control (MAC) protocol. This thesis presents four new transmission power control (TPC) techniques for MAC protocols in WSNs. These techniques are based on the interaction between sensor nodes and take into account the limitations of resources such as processing, memory and energy in the calculation of the minimum of transmission power. To evaluate these techniques, four MAC protocols had been developed: Iterative, Attenuation, AEWMA and Hybrid. The Iterative was the first MAC protocol with TPC developed exclusively for WSN. These protocols have been experimented in the Mica Motes2 platform, in diverse scenarios varying parameters such as internal and external environment, the distance among the communicating nodes, the occurrence of simultaneous transmissions, the use of multi-hop transmissions and node mobility. Results have shown that TPC protocols reduce the energy consumption by up to 57% in comparison to the protocols with fixed transmission power. Moreover, the protocols with TPC increase the throughput of the network while maintaining a very high delivery rate.
Using a Smartphone to Measure Heart Rate Changes during Relived Happiness and Anger (2013)

This study demonstrates the feasibility of measuring heart rate (HR) differences associated with emotional states such as anger and happiness with a smartphone. Novice experimenters measured higher HRs during relived anger and happiness (replicating findings in the literature) outside a laboratory environment with a smartphone app that relied on photoplethysmography.
Time-domain modeling of mode suppression in 1.3-μm Fabry-Perot lasers (1996)

Fabry-Perot lasers still comprise the bulk of lasers used in optical fiber systems. The spectral envelope, of the Fabry-Perot modes, can be modulated either deliberately or as a consequence of processing stages. This can be beneficial, in the case of modal sculpturing where specific Fabry-Perot modes are suppressed, or a hindrance in the case of poor devices. A time-domain model is used to model 1.3-μm Fabry-Perot lasers. Simulated power conserving reflective sites are introduced between sections in the model to simulate the effect of reflective sites from etch pits on the output characteristics of real lasers. Spectral modulation of the laser output is reported in agreement with previous experimental results and the strength of reflections required is investigated. We also report the use of the model to investigate the effect of fiber dispersion on the modulated laser output with different spectral mode modulation.
Comparison Between Linear Models and Survival Analysis for Genetic Evaluation of Clinical Mastitis in Dairy Cattle (2005)

Clinical mastitis was analyzed with mixed linear models (LM) and survival analysis (SA) using data from the first 3 lactations of >200,000 Swedish Holstein cows having their first calving between 1995 and 2000. The model for both methods included fixed effects of year-month and age at calving, fixed regressions of proportions of heterosis and North American Holstein genes, and random effects of herd-year at calving and sire. For the LM, clinical mastitis was defined as a binary trait measured from 10 d before to 150 d after calving. For the SA, clinical mastitis was defined either as the time period from 10 d before calving to the day of first treatment or culling because of mastitis (uncensored record) or from 10 d before to the day of next calving, culling for reasons other than mastitis, movement to a new herd, or to lactation d 240 (censored record). The heritability estimates from SA (0.03 to 0.04) were higher than those obtained with the LM (0.01 to 0.03). Consequently, the accuracies of estimated transmitting abilities were also higher for the trait analyzed with SA. The difference between estimates from the 2 methods was greater for later lactations. This study reveals the potential of analyzing clinical mastitis data with SA.
Mass Defect-Based DiLeu Tagging for Multiplexed Data-Independent Acquisition (2020)

The unbiased selection of peptide precursors makes data-independent acquisition (DIA) an advantageous alternative to data-dependent acquisition (DDA) for discovery proteomics, but traditional multiplexed quantification approaches employing mass difference labeling or isobaric tagging are incompatible with DIA. Here, we describe a strategy that permits multiplexed quantification by DIA using mass defect-based <i>N</i>,<i>N</i>-dimethyl leucine (mdDiLeu) tags and high-resolution tandem mass spectrometry (MS<sup>2</sup>) analysis. Millidalton mass differences between mdDiLeu isotopologues produce fragment ion multiplet peaks separated in mass by as little as 5.8 mDa, enabling up to 4-plex quantification in DIA MS<sup>2</sup> spectra. Quantitative analysis of yeast samples displayed comparable accuracy and precision for MS<sup>2</sup>-based DIA and MS<sup>1</sup>-based DDA methods. Multiplexed DIA analysis of cerebrospinal fluid revealed the dynamic proteome changes in Alzheimer's disease, demonstrating its utility for discovery of potential clinical biomarkers. We show that the mdDiLeu tagging approach for multiplexed DIA is a viable methodology for investigating proteome changes, particularly for low-abundance proteins, in different biological matrices.
Optimization of thin AlN sputtered films for X-band BAW resonators (2010)

We investigate the sputter growth of very thin aluminum nitride (AlN) films on iridium electrodes for high frequency filtering applications. The structure and piezoelectric activity of AlN films are assessed through XRD, FTIR, stress and frequency response measurements. A combination of a pre-deposition RF plasma treatment of the Ir bottom electrode followed by a two-step ac reactive sputtering of the AlN film allows to optimize the crystal quality and residual stress of AlN films with thicknesses as low as 160 nm. BAW resonators tuned around 8 GHz are built on top of polished Bragg reflectors composed of porous SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> and Ir layers. Material coupling factors κ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">mat</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of 6.7% and quality factors Q up to 900 are achieved. The films obtained are competitive for X-band filter fabrication.
Optical filtering and spectral measurements of radiation-induced light in plastic scintillation dosimetry (1993)

A small, water-equivalent plastic scintillation detector system has previously been developed for radiation therapy dosimetry. A light signal, proportional to dose, is generated in the scintillator and is transmitted to a remote photomultiplier tube (PMT) via optical fibres. Ionizing radiation also produces light in the fibres, which, if not properly accounted for, could limit the accuracy of the scintillator system. The fibre light is shown to have both a Cerenkov radiation and fluorescent component. The differences in the measured optical spectra of the fibre light and plastic scintillator light lead to the possibility of reducing the fibre light component by optical filtering. Optical spectral measurements of a commercially available orange-emitting plastic scintillator revealed that incomplete light-wavelength-shifting to the orange region of the visible spectrum occurs due to the size of the small scintillators that were used. Spectral measurements of orange and green scintillators with higher concentrations of wavelength-shifting fluor have been performed. Quantitative results indicate that using the highest doped orange scintillator and appropriate optical filter can decrease the fibre light contribution by about 50% when compared to the conventional blue scintillator, non-filtered case in typical radiotherapy dosimetry situations.
Application of white-light scanning interferometer on transparent thin-film measurement (2012)

A method to measure thin-film thickness, refractive index, and dispersion constants based on white-light interferometry is described. The thin-film property is retrieved from the Fourier amplitude of the white-light correlogram. The sources of errors in Fourier amplitude, which include the accuracy of wave number, light source variation in time, and illumination nonuniformity, are investigated. With all these errors reduced, the film thicknesses and refractive indices of four samples measured by white-light interferometry are within 1% of the ellipsometry results.
Inhibition of Poly(ADP-Ribose) Polymerase Enhances Cell Death and Improves Tumor Growth Delay in Irradiated Lung Cancer Models (2007)

We conclude that PARP-1 inhibition shows promise as an effective means of enhancing tumor sensitivity to radiation, and future clinical studies are needed to determine the potential of ABT-888 as a radiation enhancer.
A current ripple cancellation circuit for electrolytic capacitor-less AC-DC LED driver (2013)

This paper presents a bidirectional buck-boost current ripple cancellation circuit applied to electrolytic capacitor-less flyback LED driver with power factor correction (PFC). By operating the flyback converter in discontinuous conduction mode (DCM), high power factor can be obtained under universal input voltage range. The bidirectional buck-boost converter can minimize the twice-line-frequency output current ripple using simple open-loop pulse width modulation (PWM) control without complex control scheme, and modularization is possible for other types of converter at the PFC stage. The output current ripple can be significantly reduced without using electrolytic capacitors (E-Cap) and the power factor is near unity under universal input voltage. Finally, a 700 mA / 20 W hardware prototype is built to verify the feasibility of the proposed method.
Transition from infant‐ to adult‐like gut microbiota (2016)

Transition from an infant to an adult associated gut microbiota with age through establishment of strict anaerobic bacteria remains one of the key unresolved questions in gut microbial ecology. Here a comprehensive comparative analysis of stool microbiota in a large cohort of mothers and their children sampled longitudinally up until 2 years of age using sequencing analysis tool was presented that allows realistic microbial diversity estimates. In this work, evidence for the switch from children to adult associated microbial profile between 1 and 2 years of age was provided, suggestively driven by Bifidobacterium breve. An Operational Taxonomic Unit (OTU) belonging to B. breve was highly prevalent in the population throughout the first year of life, and was negatively associated with detection of a range of adult-like OTUs. Although an adult profile was not fully established by 2 years of age, it was demonstrated that with regards to the most prevalent OTUs, their prevalence in the child population by then already resembled that of the adult population. Taken together, it was proposed that late-colonizing OTUs were recruited at a later stage and were not acquired at birth with the recruitment being controlled by gatekeeping OTUs until the age of 1 year.