gebhart/patrepeval huggingface dataset:
From Femtoseconds to Biology: Mechanism of Bacteriorhodopsin's Light-Driven Proton Pump (1991)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
Evaluation of skin turgor and capillary refill time as predictors of dehydration in exercising dogs (2019)

OBJECTIVE To determine usefulness of skin turgor and capillary refill time (CRT) for predicting changes in hydration status of working dogs after a 15-minute exercise period. ANIMALS 9 exercise-conditioned working dogs between 8 and 108 months of age. PROCEDURES Skin tent time (SkTT; time for tented skin on the forehead to return to an anatomically normal position) and CRT (time for occluded mucous membrane capillary vessels to return to the color visible before occlusion) were measured on dogs in a field setting and by video review. Body weight (BW), SkTT, CRT, and core body temperature were measured before and after a 15-minute exercise period. Exercise challenge was performed on days 1 and 8. RESULTS Time (day 1 vs day 8) did not significantly affect results; therefore, data were pooled for the 2 trial days. Mean ± SE BW decreased (but not significantly) by 0.83 ± 0.27% after exercise. The SkTT increased significantly (both field setting and video review) after exercise. Correlation between SkTT results for the field setting and video review (r = 0.68) was significant. The CRT decreased (but not significantly) after exercise. CONCLUSIONS AND CLINICAL RELEVANCE Dogs became mildly dehydrated (mean BW loss, 0.83%) during a 15-minute exercise period, and the mild dehydration was evident as a visually detectable change in skin turgor. Monitoring the SkTT appeared to be a useful strategy for predicting small shifts in hydration status of dogs during exercise. The CRT decreased and was not a significant predictor of a change in hydration status.
Cutting care clusters: the creation of an inverse pharmacy care law? An area-level analysis exploring the clustering of community pharmacies in England (2018)

Clustering of community pharmacies in England is common, although there is a positive trend between community pharmacy clustering and social deprivation, whereby clustering is more significant in areas of high deprivation. Arrangements for future community pharmacy funding should not solely focus on distance from one pharmacy to another as means of determining funding allocation, as this could penalise community pharmacies in our most deprived communities, and potentially have a negative effect on other healthcare providers, such as general practitioner and accident and emergency services.
Adaptor device for shortening guide catheters to access distal lesions in coronary angioplasty (1993)

One of the challenges in interventional cardiology is accessing distal stenoses in both native coronary arteries and bypass grafts. This article reports the fabrication and use of an adaptor device that can be connected to the proximal segment of a shortened guide catheter for easier and safer access to these distal lesions.
Potential Deleterious Effect ofß-Adrenergic Stimulation During Warm-Blood Cardioplegia in Rabbit Hearts (2001)

We hypothesized that beta-adrenergic stimulation with isoproterenol during continuous normothermic cardioplegic arrest would enhance the regenerative and regulatory function of the myocardium, resulting in improved cardiac function. We studied isolated rabbit hearts paced at approximately 200 beats per minute (bpm) and perfused by a support rabbit. We measured ventricular pressure over a range of ventricular volumes to determine maximal elastance (Emax) at baseline and 20 and 45 min after discontinuation of cardioplegia. Myocardial oxygen consumption (MVO2) measurements were performed simultaneously and during cardioplegic arrest. Hearts were prospectively randomized to receive either isoproterenol at 0.1 M or control in blinded fashion for 10 min during a 1-h continuous warm-blood cardioplegic arrest. Compared to control hearts, isoproterenol-treated hearts had trends toward longer time to first spontaneous heartbeat (control 141 +/- 43 vs. isoproterenol 200 +/- 74 s, p = .07), and longer time to capture of atrial pacing (control 214 +/- 52 vs. isoproterenol 288 +/- 91 s, p = .06). There was no difference observed in the MVO2 between isoproterenol-treated and control groups of hearts. MVO2 decreased during cardioplegia (p < .01), but there was no significant change in MVO2 during isoproterenol infusion during cardioplegic arrest. There was a significant reduction in Emax compared to baseline 20 min after discontinuation of cardioplegic arrest in both groups (control 7.3 +/- 1.7 mm Hg/microL vs. 9.0 +/- 1.7 mm Hg/microL, p = .02, isoproterenol-treated 6.8 +/- 2.8 mm Hg/microL vs. 8.2 +/- 2.6 mm Hg/microL, p = .01, respectively), with recovery of Emax by 45 min in control hearts only. We conclude that exposure of hearts to isoproterenol during warm cardioplegic arrest has a deleterious effect that may be mediated through mechanisms independent of increased myocardial oxygen consumption.
Incidence and Predictors of Atrial Fibrillation Progression (2019)

Background The incidence and predictors of atrial fibrillation (AF) progression are currently not well defined, and clinical AF progression partly overlaps with rhythm control interventions (RCIs). Methods and Results We assessed AF type and intercurrent RCIs during yearly follow-ups in 2869 prospectively followed patients with paroxysmal or persistent AF. Clinical AF progression was defined as progression from paroxysmal to nonparoxysmal or from persistent to permanent AF. An RCI was defined as pulmonary vein isolation, electrical cardioversion, or new treatment with amiodarone. During a median follow-up of 3 years, the incidence of clinical AF progression was 5.2 per 100 patient-years, and 10.9 per 100 patient-years for any RCI. Significant predictors for AF progression were body mass index (hazard ratio [HR], 1.03; 95% CI, 1.01-1.05), heart rate (HR per 5 beats/min increase, 1.05; 95% CI, 1.02-1.08), age (HR per 5-year increase 1.19; 95% CI, 1.13-1.27), systolic blood pressure (HR per 5 mm Hg increase, 1.03; 95% CI, 1.00-1.05), history of hyperthyroidism (HR, 1.71; 95% CI, 1.16-2.52), stroke (HR, 1.50; 95% CI, 1.19-1.88), and heart failure (HR, 1.69; 95% CI, 1.34-2.13). Regular physical activity (HR, 0.80; 95% CI, 0.66-0.98) and previous pulmonary vein isolation (HR, 0.69; 95% CI, 0.53-0.90) showed an inverse association. Significant predictive factors for RCIs were physical activity (HR, 1.42; 95% CI, 1.20-1.68), AF-related symptoms (HR, 1.84; 95% CI, 1.47-2.30), age (HR per 5-year increase, 0.88; 95% CI, 0.85-0.92), and paroxysmal AF (HR, 0.61; 95% CI, 0.51-0.73). Conclusions Cardiovascular risk factors and comorbidities were key predictors of clinical AF progression. A healthy lifestyle may therefore reduce the risk of AF progression.
(Invited) Chemisorption Reaction Mechanisms for Atomic Layer Deposition of High-k Oxides on High Mobility Channels (2010)

For next generation CMOS technology nodes, new channel materials, such as Ge and III/V semiconductors, are investigated because of their higher intrinsic carrier mobility as compared to Si. In this work, we have studied the chemisorption reaction mechanisms for Atomic Layer Deposition (ALD) of the high-k dielectric Al2O3 on S-passivated Ge by means of ab initio calculations. The calculations provide insight into the specific interactions occurring during gate stack formation and the character of the bonds at the Ge interface.
In Vitro Models for Investigation of the Effects of Acute Mechanical Injury on Cartilage (2001)

Traumatic injury to a joint is known to increase the risk for the development of secondary osteoarthritis, but it is unclear how this process occurs. The existence of such a discrete event that can lead to an increased risk of osteoarthritis has spurred interest in developing in vitro models of traumatic joint injury. The current authors review some of the recent insights gained from these model systems into the pathogenesis of osteoarthritis, including the evidence for an initial, irreversible insult to chondrocytes during mechanical injury, the occurrence of apoptotic chondrocyte death, and attempts to identify the effects of trauma on chondrocyte metabolic response. Results also are presented from the authors' ongoing studies of the degradative pathways initiated by traumatic mechanical loads, the mechanism by which chondrocytes are affected during compression, and possible contributions of the joint capsule to posttraumatic cartilage degradation.
Bacterial vesicles block viral replication in macrophages via TLR4-TRIF-axis (2023)

Gram-negative bacteria naturally secrete nano-sized outer membrane vesicles (OMVs), which are important mediators of communication and pathogenesis. OMV uptake by host cells activates TLR signalling via transported PAMPs. As important resident immune cells, alveolar macrophages are located at the air-tissue interface where they comprise the first line of defence against inhaled microorganisms and particles. To date, little is known about the interplay between alveolar macrophages and OMVs from pathogenic bacteria. The immune response to OMVs and underlying mechanisms are still elusive. Here, we investigated the response of primary human macrophages to bacterial vesicles (Legionella pneumophila, Klebsiella pneumoniae, Escherichia coli, Salmonella enterica, Streptococcus pneumoniae) and observed comparable NF-κB activation across all tested vesicles. In contrast, we describe differential type I IFN signalling with prolonged STAT1 phosphorylation and strong Mx1 induction, blocking influenza A virus replication only for Klebsiella, E.coli and Salmonella OMVs. OMV-induced antiviral effects were less pronounced for endotoxin-free Clear coli OMVs and Polymyxin-treated OMVs. LPS stimulation could not mimic this antiviral status, while TRIF knockout abrogated it. Importantly, supernatant from OMV-treated macrophages induced an antiviral response in alveolar epithelial cells (AEC), suggesting OMV-induced intercellular communication. Finally, results were validated in an ex vivo infection model with primary human lung tissue. In conclusion, Klebsiella, E.coli and Salmonella OMVs induce antiviral immunity in macrophages via TLR4-TRIF-signaling to reduce viral replication in macrophages, AECs and lung tissue. These gram-negative bacteria induce antiviral immunity in the lung through OMVs, with a potential decisive and tremendous impact on bacterial and viral coinfection outcome. Video Abstract.
Point Defect Generation Probability in Rare-Earth Permanent Magnets in Radiation Environments via First-Principle Calculations (2022)

In recent years, rare-earth permanent magnets, including Nd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sub> B and Sm <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</sub> , which are used in environments with high radiation, such as in electric motors for space equipment and robots operating in nuclear reactors, have become increasingly important. However, the demagnetization of the rare-earth permanent magnets induced by exposure to radiation has become a serious issue. In particular, when high-energy neutrons collide with the atoms in the magnet, the atoms can be removed and point defects can be generated. The spin fluctuations caused by point defects result in demagnetization of the rare-earth permanent magnets. In this study, we investigate via first-principle calculations, the probability of generation of point defects and the change in the magnetic moment in Nd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sub> B and Sm <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</sub> that occurs as a result of the point defect creation. We find that the generation probability of the point defects is very similar in both rare-earth magnets. The attenuation of the magnetic moment in Sm <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</sub> was found to be considerably smaller than that of Nd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sub> B. Thus, we conclude that the radiation resistance of the magnetic properties of Sm <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</sub> is higher than that of Nd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</sub> B.
A Maximal Correlation Approach to Imposing Fairness in Machine Learning (2020)

As machine learning algorithms grow in popularity and diversify to many industries, ethical and legal concerns regarding their fairness have become increasingly relevant. We explore the problem of algorithmic fairness, taking an information-theoretic view. The maximal correlation framework is introduced for expressing fairness constraints and shown to be capable of being used to derive regularizers that enforce independence and separation-based fairness criteria, which admit optimization algorithms for both discrete and continuous variables which are more computationally efficient than existing algorithms. We show that these algorithms provide smooth performance-fairness tradeoff curves and perform competitively with state-of-the-art methods on both discrete datasets (COMPAS, Adult) and continuous datasets (Communities and Crimes).
Manipulation of Cannabinoid Biosynthesis via Transient RNAi Expression (2021)

<i>Cannabis sativa</i> L. produces unique phytocannabinoids, which are used for their pharmaceutical benefits. To date, there are no reports of <i>in vivo</i> engineering targeting the cannabinoid biosynthesis genes to greater elucidate the role each of these genes play in synthesis of these medically important compounds. Reported here is the first modulation of cannabinoid biosynthesis genes using RNAi <i>via</i> agroinfiltration. Vacuum infiltrated leaf segments of the Cannbio-2 <i>C. sativa</i> strain, transfected with different RNAi constructs corresponding to <i>THCAS, CBDAS</i>, and <i>CBCAS</i> gene sequences, showed significant downregulation of all cannabinoid biosynthesis genes using real-time quantitative PCR. Using RNAi, significant off-targeting occurs resulting in the downregulation of highly homologous transcripts. Significant (<i>p</i> < 0.05) downregulation was observed for <i>THCAS</i> (92%), <i>CBDAS</i> (97%), and <i>CBCAS</i> (70%) using pRNAi-GG-<i>CBDAS-UNIVERSAL</i>. Significant (<i>p</i> < 0.05) upregulation of <i>CBCAS</i> (76%) and non-significant upregulation of <i>THCAS</i> (13%) were observed when transfected with pRNAi-GG-<i>CBCAS</i>, suggesting the related gene's ability to synthesize multiple cannabinoids. Using this approach, increased understanding of the relationship between cannabinoid biosynthesis genes can be further elucidated. This RNAi approach enables functional genomics screens for further reverse genetic studies as well as the development of designer cannabis strains with over-expression and/or downregulation of targeted cannabinoid biosynthesis genes. Functional genomics screens, such as these, will further provide insights into gene regulation of cannabinoid biosynthesis in <i>Cannabis</i>.
A CD14 Domain with Lipopolysaccharide‐Binding and ‐Neutralizing Activity (2006)

The interaction of lipopolysaccharide with CD14 plays a key role in signaling that activates an early defense against pathogens but also contributes to the development of sepsis and septic shock. Here we have mapped the entire 356-amino-acid protein with synthetic 20-amino-acid peptides and have identified a new lipopolysaccharide-binding domain with a strong LPS-neutralizing activity. Moreover, analysis of the structure-activity relationship of this peptide, which corresponds to amino acids 81-100 of human CD14, revealed that leucines 87, 91, and 94 are essential for these activities. The functional relevance of these residues was confirmed by cellular expression of mutant CD14 proteins that are no longer able to bind LPS. Furthermore, the peptide provided a basis for the generation of highly soluble analogues with stronger lipopolysaccharide-neutralizing activity.
Disfluency Detection for Spoken Learner English (2019)

One of the challenges for computer aided language learning (CALL) is providing high quality feedback to learners. An obstacle to improving feedback is the lack of labelled training data for tasks such as spoken”grammatical” error detection and correction, both of which provide important features that can be used in downstream feedback systems One approach to addressing this lack of data is to convert the output of an automatic speech recognition (ASR) system into a form that is closer to text data, for which there is significantly more labelled data available. Disfluency detection, locating regions of the speech where for example false starts and repetitions occur, and subsequent removal of the associated words, helps to make speech transcriptions more text-like. Additionally, ASR systems do not usually generate sentence-like units, the output is simply a sequence of words associated with the particular speech segmentation used for coding. This motivates the need for automated systems for sentence segmentation. By combining these approaches, advanced text processing techniques should perform significantly better on the output from spoken language processing systems. Unfortunately there is not enough labelled data available to train these systems on spoken learner English. In this work disfluency detection and”sentence” segmentation systems trained on data from native speakers are applied to spoken grammatical error detection and correction tasks for learners of English. Performance gains using these approaches are shown on a free speaking test.
Possible direct involvement of the active‐site [4Fe–4S] cluster of the GcpE enzyme from Thermus thermophilus in the conversion of MEcPP (2006)

The GcpE enzyme converts 2-C-methyl-D-erythritol-2,4-cyclodiphosphate (MEcPP) into (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) in the penultimate step of the DOXP pathway for isoprene biosynthesis. Purification of the enzyme under exclusion of air leads to a preparation that contains solely [4Fe-4S] clusters. Kinetic studies showed that in the presence of the artificial reductant dithionite and MEcPP a new transient iron-sulfur-based signal is detected in electron paramagnetic resonance (EPR) spectroscopy. Similarity of this EPR signal to that detected in ferredoxin:thioredoxin reductase indicates that during the reaction an intermediate is directly bound to the active-site cluster.
Laboratory experimental results of an adaptive modulation/TDMA/TDD for wireless multimedia communication systems (2002)

This paper reports laboratory experimental results of a time division multiple access/time division duplex (TDMA/TDD) based adaptive modulation system to verify feasibility and its usefulness for future wireless multimedia communication systems. The developed system employs a symbol rate and modulation level controlled adaptive modulation in which the modulation scheme is selected from full-rate 64-ary quadrature amplitude modulation (64 QAM), full-rate 16 QAM, full-rate quaternary phase shift keying (QPSK), 1/2-rate QPSK, 1/4-rate QPSK, 1/8-rate QPSK and no transmission according to the expected channel condition for the transmitted signal. The experimental results confirm that the developed system is very effective in achieving high quality and high bit rate transmission of around 1 Mbit/s without any special anti-frequency selective fading techniques even under frequency selective fading conditions with its d delay spread of less than 250 ns and f/sub d/ of less than 10 Hz.
Synthesis, Anion‐Binding Properties, and In Vitro Anticancer Activity of Prodigiosin Analogues (2005)

Pro and anti: Recognition of chloride ion and through-membrane H+/Cl− ion transport (“symport”) could account for the biological effects (anticancer activity) of prodigiosin, as inferred from model studies involving pyrrole-based anion receptors designed to mimic the key features of this naturally occurring pigment (see picture). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501740_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Suppl Fig 2 from Intrathecal Viral Vector Delivery of Trastuzumab Prevents or Inhibits Tumor Growth of Human HER2-Positive Xenografts in Mice (2023)

&lt;p&gt;Biodistribution of vector genome copies in brain&lt;/p&gt;
Thermal Analysis of In-Situ Thermoplastic-Matrix Composite Filament Winding (1991)

In filament winding of thermoplastics, localized melting/solidification can reduce the residual stresses and allow for improved dimensional stability and performance. This paper presents a three-dimensional thermal analysis for melting and consolidating impregnated tows in the presence of a local heat source during filament winding of thermoplastic composites. The analysis is performed using an Eulerian approach. The anisotropy of the filament wound woven structure is modeled as an orthotropic domain employing the concept of angle-ply sublaminates. The effective orthotropic conductivity tensor incorporates the effect of winding angle. The governing equations are discretized in a nonuniform mesh domain and solved using a finite difference approach. The processing parameters, such as winding angle, winding speed, and heat input, as well as material properties, are incorporated into the analysis. The results show large thermal gradients in the vicinity of the consolidation point. The effects of winding speed and heat input are investigated, and the overall thermal characterization of the process is discussed. The accuracy of the numerical method is assessed by comparing the results of a test problem with an available analytical solution.
Edge breakdown issues in field emission displays (2001)

This paper addresses edge breakdown issues in vacuum gap structures similar to field emission displays, both from a theoretical and practical point of view. Several unique solutions have been developed. After using these technologies, the breakdown voltage of a 750 /spl mu/m plain-vacuum gap formed by two thin-film electrodes was improved from /spl sim/16 to /spl sim/24 kV for the first run, and /spl sim/20 to 28 kV for the conditioned regime. The mechanism of breakdown in a plain vacuum gap is discussed.