gebhart/patrepeval huggingface dataset:
Immunologic Reconstitution Through 6 Years in Antiretroviral-Naïve Subjects Treated with Lopinavir/ritonavir (LPV/r) (2005)

A Landay, B da Silva, M King, M Albrecht, C Benson, J Eron, M Glesby, R Gulick, C Hicks, H Kessler, R Murphy, M Thompson, AC White, P Wolfe, F McMillan, N Braun, D Calhoun and G Hanna Rush Med. Coll., United States; Harvard U, United States; Colorado U, United States; U North Carolina, United States; Cornell U, United States; Duke U, United States; Northwestern U, United States; ARCA Atlanta, United States; Baylor Coll. Med., United States; Pacific Oaks Res., United States; Abbott Laboratories, United States Third IAS Conference on HIV Pathogenesis and Treatment 24–27 July 2005, Rio de Janeiro, Brazil WePe16.7B04
Passband Control of Lightly Damped Systems With Mode Separation (2008)

This paper deals with the regulation and stabilization of lightly damped systems under plant uncertainty. A controller consisting of a neural-network-based mode separator together with a modular passband tuning regulator is proposed. The mode separator generates the in-phase components of the plant utilized by the passband tuning regulator to maintain closed-loop stability and asymptotic regulation. This combined controller is robust and requires minimal plant information to operate. A synthesis procedure is outlined in this paper to summarize the design steps in a systematic manner. Finally, the application of the passband controller to the stabilization of a magnetic leadscrew is considered. Resonance is shown to be completely eliminated. The stabilization time of the transient response is also significantly reduced, confirming the feasibility of the controller.
Smoking status and treatment outcome in patients with pancreatic cancer. (2016)

e15676 Background: Tobacco smoking is a recognized risk factor for pancreatic cancer (PC). The aim of the study was to characterize clinical features, treatment, molecular abnormalities and survival of patients with PC in relation to smoking status. Methods: Data for 299 patients with PC diagnosed and/or treated in the Princess Margaret Cancer Center/University Health Network between 2008-2015 was obtained retrospectively from the electric patient records. Results: There were 141 females (47%), 158 males (53%), median age was 64 years (range: 28-89). Median follow-up was 12.2 months (range: 0.8-82.4). The majority of patients were never smokers (50%) followed by ex- (38%) and current smokers (12%). Of all the patients with known family history, 11% had a history of PC. Among 182 patients with known BRCA status, 14% had germline mutations. Most patients had adenocarcinoma (98%) and presented in stage IV (40%), followed by locally advanced (LO) unresectable (30%) and LO resectable (30%) disease. Smoking did not impact stage at diagnosis. Overall survival (OS) did not differ between never-, ex- and current smokers, with one year OS rates of 51%, 55% and 55%. Smoking pack years was not significantly associated with survival. Smoking was associated with male sex (p = 0.0053), higher body surface area (BSA) (p = 0.00063), and being a BRCA carrier (p = 0.01). Never smokers were more likely to have experienced weight loss at diagnosis (p = 0.027). In multivariable analysis old age ( > 64 vs. < 64; HR = 1.34; 95% CI: 1.01-1.8; p = 0.045) and poor performance status (ECOG 2-3 vs. 0; HR = 1.92; 95% CI: 1.24-3; p = 0.0038)were associated with poorer survival. Metastatic (vs. resectable) disease at diagnosis was associated with poorer survival, however the effect was largest in early follow-up and diminished with time (HR = 6.88, 95% CI: 3.35-14.14; p < .0001, with time HR = 0.95, 95% CI: 0.91-1, p = 0.031).After adjusting for age, BSA, ECOG and stage at diagnosis, smoking status was not significantly associated with survival (HR = 0.89; 95% CI = 0.67-1.18; p = 0.43). Conclusions: Smoking status does not affect treatment outcome in patients with pancreatic adenocarcinoma. Association of germline BRCA and smoking warrants validation studies.
Transfection of murine dendritic cell line (JAWS II) by a nonviral transfection reagent (2003)

Dendritic cells are the most potent antigen-presenting cells that initiate and modulate the host immune system. Based on their immunostimulatory activity, a variety of strategies have been developed to use dendritic cells as vaccines and immunotherapeutic agents against infection and cancer. Genetically modified dendritic cells are useful for immunotherapeutic purposes because of their sustained activity in vivo. However, transfection of dendritic cells with plasmid DNA has been very difficult. While the viral transfection is associated with nonspecific activation of dendritic cells, commonly used nonviral transfection reagents have a low efficiency of transfection. Here we describe an improved, simple, less time-consuming transfection protocol using the nonviral nonliposomal lipid polymer, TransIT-TKO transfection reagent, for transfecting murine dendritic cells (JAWS II) with the gene that encodes Coccidioides immitis antigen 2 (Ag2). The JAWS II cells were cotransfected with pHYG-enhanced green fluorescent protein (EGFP) and pVR1012-C. immitis Ag2 plasmid DNAs using TransIT-TKO reagent. We reproducibly obtained 30%-50% transfection efficiency. The transfected cells maintained their immature phenotype and were functionally active. In addition, the flexibility of this agent for expressing multiple antigens (GFP and C. immitis Ag2) offers an advantage of delivering multiple immunogens.
The Degradome database: mammalian proteases and diseases of proteolysis (2008)

The degradome is defined as the complete set of proteases present in an organism. The recent availability of whole genomic sequences from multiple organisms has led us to predict the contents of the degradomes of several mammalian species. To ensure the fidelity of these predictions, our methods have included manual curation of individual sequences and, when necessary, direct cloning and sequencing experiments. The results of these studies in human, chimpanzee, mouse and rat have been incorporated into the Degradome database, which can be accessed through a web interface at http://degradome.uniovi.es. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This web site also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes.
Order parameters of the orientation distribution of collagen fibers in Achilles tendon by <sup>1</sup>H NMR of multipolar spin states (2003)

The angular distribution function of collagen fibrils in a sheep Achilles tendon was investigated by (1)H NMR of multipolar spin states represented by dipolar-encoded longitudinal magnetization and double-quantum filtered signals. For the first time the angular distribution function based on the Legendre moment expansion is used. Order parameters were obtained from the anisotropy of (1)H residual dipolar couplings of bond water, which were determined model-free from the excitation efficiency of the multipolar spin states and from double-quantum filtered line splitting. The orientation distribution function of collagen fibrils in Achilles tendon measured from the anisotropy of the residual dipolar couplings is characterized by the average values of beta0 = 1.8+/-0.2 degrees and order parameters [P2] = 0.93+/-0.04, [P4] = 0.78+/-0.04 and [P6] = 0.58+/-0.04. The order of many biological tissues in the presence of ageing, injuries or regeneration can be quantified by the order parameters of the angular distribution function.
Opportunities for improving livestock production with e-Management systems (2013)

There is increased interest in hardware and software that can support e-Management for grassland-based livestock industries. Managers of grazing livestock were early adopters of radio frequency identification (RFID) technologies automatically monitoring individual animal performance. Recent developments of remote sensing, automated individual recording and management, location based systems, improved data transfer and technologies that can be used in more extensive grazing systems are providing new opportunities for the development of e-Management systems. There is a need for better data integration and systems that can provide the best available information to enable better decision-making. For greater industry adoption of more integrated e-Management systems, there needs to be a clear economic value. With increased on farm monitoring and the expansion of digital data sources, grazing livestock production systems have the opportunity to expand production efficiency through the implementation of e-Management.
Characteristics and early outcomes of patients hospitalised for COVID-19 in North Zealand, Denmark. (2020)

not relevant.
Nanofibers: Click Synthesis, Aggregation‐Induced Emission and Chirality, Circularly Polarized Luminescence, and Helical Self‐Assembly of a Leucine‐Containing Silole (Small 47/2016) (2016)

The synthesis of a chiral fluorescent silole derivative containing l-leucine methyl ester moiety (Silole–Leu) is reported by B. S. Li, B. Z. Tang, co-workers on page 6593. Silole–Leu exhibits aggregation-induced emission and circular dichroism, and circular polarized luminescence. Silole–Leu is endowed with the ability to self-assemble into nano/micro helical luminescent fibers and their dimensions can be tuned by adjusting the ratio and volume of the mixed solvents for assembling.
Origin in<i>Acinetobacter gyllenbergii</i>and dissemination of aminoglycoside-modifying enzyme AAC(6′)-Ih (2015)

We have found the origin of aac(6')-Ih in A. gyllenbergii, a species isolated, although rarely, in humans, and documented that dissemination of this gene is restricted to the Acinetobacter genus.
S4‐04‐06: Dimebon®: A Clinically Promising Drug for Alzheimer's Disease, Regulates Amyloid‐Beta Metabolism in Cultured Cells, In Isolated Nerve Terminals, and In the Interstitial Fluid of the Living Rodent Brain (2009)

Recent evidence indicates that the retired Russian antihistamine Dimebon® (dimebolin) improves cognitive function in aged rodents and in humans suffering from mild to moderate Alzheimer's disease (AD). A recent screen against a set of biochemical targets indicated that Dimebon® inhibits alpha-adrenergic receptors (alpha-1A, alpha-1B, alpha-1D, alpha-2A), histamine H1 and H2 receptors, and serotonin 5-HT 2c, 5-HT 5A, and 5-HT 6 receptors with high affinity (Wu et al., Molec Neurodeg, 2008, 3: 15doi:10.1186/1750-1326-3-15). Dimebon® has also been shown to modulate Ca2+ flux, apoptosis, and mitochondrial stability. Given the clinical benefit, and given the known modulation of A-beta metabolism by neurotransmitters and by mitochondrial function, we assessed the ability of Dimebon® to modulate levels of APP metabolites including A-beta in a series of in vitro and in vivo experimental systems. Under control conditions or following Dimebon® treatment, we measured A-beta levels in either: (1) the conditioned media of SweAPP-overexpressing cultured N2a mouse neuroblastoma cells; (2) the releasate from isolated nerve terminals from TgCRND8 mice overexpressing Swe/Indiana APP, or (3) the interstitial fluid (ISF) of the brains of freely moving Tg2576 SweAPP-overexpressing transgenic mice. Acute treatment with Dimebon® increased A-beta levels in the releasate from TgCRND8 nerve terminals and in the ISF of freely moving Tg2576 transgenic mice. In media conditioned by SweAPP N2a cells overnight in the presence of drug, Dimebon® either had no effect on A-beta or lowered A-beta. Since questions have been raised regarding the nature of Dimebon® preparations, we performed these studies using Dimebon® from two independent vendors; both gave similar results. Elevation of A-beta release from isolated nerve terminals and elevation of ISF A-beta levels are unexpected phenomena to associate with a clinically beneficial AD drug. Further study is required to elucidate the molecular mechanism underlying the acute regulation of A-beta metabolism by Dimebon®. Chronic Dimebon® exposure also merits study. Dimebon® may be a useful chemical probe for advancing our understanding of the role of A-beta in AD and for identifying unexplored druggable mechanisms in the molecular pathogenesis of AD.
Self-consistent nonlocal linear-response theory of a relativistic electron gas (2003)

The displaced charge in an initially homogeneous electron gas due to a weak perturbing potential as calculated by March and Murray was generalized to include relativistic effects by Baltin and March. This latter result is here used to study the relativistic corrections to the static Lindhard dielectric function. An analytic generalization of the Lindhard function to the second order in the Compton wavelength is presented.
Augmented creativity (2015)

Augmented Reality (AR) holds unique and promising potential to bridge between real-world activities and digital experiences, allowing users to engage their imagination and boost their creativity. We propose the concept of Augmented Creativity as employing ar on modern mobile devices to enhance real-world creative activities, support education, and open new interaction possibilities. We present six prototype applications that explore and develop Augmented Creativity in different ways, cultivating creativity through ar interactivity. Our coloring book app bridges coloring and computer-generated animation by allowing children to create their own character design in an ar setting. Our music apps provide a tangible way for children to explore different music styles and instruments in order to arrange their own version of popular songs. In the gaming domain, we show how to transform passive game interaction into active real-world movement that requires coordination and cooperation between players, and how ar can be applied to city-wide gaming concepts. We employ the concept of Augmented Creativity to authoring interactive narratives with an interactive storytelling framework. Finally, we examine how Augmented Creativity can provide a more compelling way to understand complex concepts, such as computer programming.
Patient Interpretation of Neuropathy (PIN) Questionnaire (2006)

The 39-item PIN questionnaire is a reliable and valid measure of patients' cognitive and emotional representations of neuropathy affecting foot self-care.
RANDOMIZED, DOUBLE-BLIND, PLACEBO (PBO)-CONTROLLED, SINGLE- AND MULTIPLE-DOSE PHASE 1 STUDY OF VE202, A DEFINED BACTERIAL CONSORTIUM FOR TREATMENT OF IBD: SAFETY AND COLONIZATION DYNAMICS OF A NOVEL LIVE BIOTHERAPEUTIC PRODUCT (LBP) IN HEALTHY ADULTS (2022)

Abstract IBD patients can have reduced gut commensal abundance, relative expansion of pro-inflammatory taxa, and reduced microbial diversity and short-chain fatty acid production. FMT leads to clinical remission in some UC patients, but is a complex, nonscalable process with inconsistent composition/quality that has led to death from transmission of pathogens undetected in screening. VE202 is a rationally defined LBP of 16 beneficial Clostridia from clusters IV, XIVa, and XVIII, with properties including association with healthy human microbiomes, promotion of colonic Treg cells, production of beneficial and immunoregulatory metabolites, efficacy in mouse colitis models, and lack of overt pathogenic or toxigenic features. These properties could help restore a healthy microbiome in UC patients. Another rationally defined LBP, VE303, showed activity in a Phase 2 study for prevention of recurrentC. difficile. The goal of the current Phase 1 study was to evaluate safety and colonization of VE202, to inform planned Phase 2 trials in UC patients. METHODS: After 5 days of vancomycin pretreatment at 125mg po QID to decrease gut microbial burden, 31 healthy adults received 1 dose at 2 dosage levels (6 VE202, 3 PBO per dosage level) or a 14-day course (9 VE202, 4 PBO) of the lower dose. Each VE202 delayed-release enteric capsule contained ∼1x109 CFU of bacteria. Safety was monitored through Week 12, with phone follow-up at Week 24. Stool was collected for LBP strain detection and exploratory microbiome, metabolomic, and immune markers. RESULTS: VE202 was well tolerated with no dose-dependent pattern of AEs. The only MedDRA organ classes with ≥20% reported AEs in VE202 recipients were: —Single-dose cohorts (N=12): GI (n=6; 50%), nervous system (n=4; 33.3%), investigations and infections/infestations (n=3 each; 25%) —14-day cohort (N=9): GI (n=5; 55.6%), general/administration site, musculoskeletal/connective tissue and nervous system (n=3 each; 33.3%), and skin/subcutaneous tissue (n=2; 22.2%) In VE202 recipients (N=21), the only AEs seen in ≥10% of subjects were abdominal discomfort, diarrhea, headache (n=4 each; 19.0%), and fatigue (n=3; 14.3%). No severe AEs or clinically significant trends in lab values were seen. Two SAEs, neither treatment-related, occurred several weeks after completion of VE202 dosing: abdominal pain caused by a suspected passed bile duct stone (Day 71) and hip pain leading to hip replacement (Day 120). Sustained VE202 strain detection (Figure 1) and relative abundance (Figure 2) in the vancomycin-perturbed gut was seen as soon as Day 2, sustained through 2 weeks after dosing completion, then declined slowly but remained substantially above baseline through Week 24. A dose- and duration-dependent trend in colonization was seen. CONCLUSION: VE202 is well tolerated in healthy adults and provides robust, durable, abundant colonization of LBP strains.
Choice of reference in analysis of CAEPs to auditory and audiovisual stimuli (2012)

A general principle of EEG measurements is that each recorded channel represents the difference in activity between two electrodes on the head. Use of different reference schemes between studies may contribute, among other factors, to inconsistencies of findings (Hagemann, 1998). This study investigates the effect of choice of reference on the CAEPs to auditory and audiovisual stimuli in normal hearing adults. The CAEPs were recorded to natural speech tokens presented as auditory, visual and audiovisual stimuli. The CAEPs were recorded with FCz as a reference and re-referenced offline to right mastoid, left mastoid, mean mastoids and an average reference respectively. The amplitude of the average reference waveforms were significantly smaller compared to the other references. Three of the four references (right, left and mean mastoids) showed a temporal facilitation with shorter latencies for N1 in the audiovisual condition. No latency differences were found for the average reference. All references showed a modality effect with audiovisual stimuli resulting in significantly enhanced N1/P2 amplitudes compared to auditory. The results suggest that the choice of reference has a significant effect on the temporal analysis of CAEPs and emphasise the importance of indication and justification of any choice of reference.
Effects of Food Storage and Handling on Blow Fly <i>(Lucilia sericata)</i> Eggs and Larvae (2006)

ABSTRACT: Flies can cause food‐borne disease by transmitting pathogenic microorganisms into the food we eat or by being ingested themselves (“intestinal myiasis”), usually as eggs or larvae contaminating our food. Because eggs and larvae can easily contaminate our food during harvesting, handling, and preparation, this series of experiments was undertaken to define the food preparation conditions that would be necessary to kill contaminating blow fly eggs and larvae. Replicate samples of Lucilia (= Phaenicia) sericata (Meigen) eggs and larvae were exposed to increasing periods of freezing, refrigeration, baking, boiling, frying, and microwaving. Survivors were counted every 6 to 48 h thereafter, and the exposures that were lethal to 50% (LE 50 ), 90% (LE 90 ), and 99% of our samples (LE 99 ) were calculated. All of the tested food‐preparation methods killed most or all of the eggs and larvae when exposed for durations typically associated with food preparation. These results indicate that the common methods of food preparation should adequately kill all L. sericata eggs and larvae that may be associated with raw meat. Freezing and extended refrigeration also killed all eggs and larvae. This supports the belief, hitherto unproven, that contamination of cooked meat products most likely occurs at or after the point of retail‐consumer contact.
Recombinant Variants of Tissue-Type Plasminogen Activator Containing Amino Acid Substitutions in the Finger Domain (1992)

Tissue-type plasminogen activator (t-PA) is a fibrin-specific agent which has been used to treat acute myocardial infarction. In an attempt to clarify the determinants for its rapid clearance in vivo and high affinity for fibrin clots, we produced five variants containing amino acid substitutions in the finger domain, at amino acid residues 7-9, 10-14, 15-19, 28-33, and 37-42. All the variants had a prolonged half-life and a decreased affinity for fibrin of various degrees. The 37-42 variant demonstrated about a 6-fold longer half-life with a lower affinity for fibrin. Human plasma clot lysis assay estimated the fibrinolytic activity of the 37-42 variant to be 1.4-fold less effective than that of the wild-type rt-PA. In a rabbit jugular vein clot lysis model, doses of 1.0 and 0.15 mg/kg were required for about 70% lysis in the wild-type and 37-42 variant, respectively. Fibrinogen was degraded only when the wild-type rt-PA was administered at a dose of 1.0 mg/kg. These findings suggest that the 37-42 variant can be employed at a lower dosage and that it is a more fibrin-specific thrombolytic agent than the wild-type rt-PA.
Investigation of Catalyst Durability under Fuel Cell Operation with Reduced Cathode Platinum Loadings (2012)

Abstract not Available.
RGB detectors on compressive snapshot multi-spectral imagers (2015)

The coded aperture snapshot spectral imager (CASSI) system has been demonstrated to produce spectral images using just a single snapshot taken by a monochrome image sensor. In this paper, we introduce the use of color image sensors in CASSI to include the spectral sensitivity of the image sensor pixels to account for color and then investigate the impact on image quality. We analyze the use of the traditional Bayer color filter array image sensor, and the novel Foveon image sensor which stacks red, green, and blue pixels on top of one another. Several simulations on different 3D spatio-spectral databases show improvements of up to 3 dBs in terms of PSNR over traditional monochrome sensors.
Automatic prosody labeling using both text and acoustic information (2003)

Prosody is an important factor for a high quality text-to-speech (TTS) system. The prosody is often described with a hierarchical structure. So the generation of the hierarchical prosody structure is very important both in the corpus building and the run-time text analysis. But the prosody labeling procedure is laborious and time consuming. Moreover, to keep the consistence between different labelers and even the same labeler in different time is difficult. In this paper an automatic prosody labeling system is presented, in which the decision tree plus Viterbi decoding framework proposed Wightman and Ostendorf (1994) is used. In the system, not only the acoustic information but also the text information such as the part-of-speech (POS) of a word is used. A prosody model is built up using the automatically labeled corpus for our Mandarin TTS system. Listening test shows that the automatic prosody labeling system works pretty well.