gebhart/patrepeval huggingface dataset:
The impact of poorly applied human resources policies on individuals and organisations (2023)

Background/Aims Recent incidents have raised awareness about how corporate decisions and behaviour can negatively affect the health and wellbeing of healthcare professionals. This article uses a case study to explore the harm that failing to follow human resources procedures can cause to individuals, organisational culture and effectiveness, and make recommendations to improve practice. Methods Seven experts from a range of professional backgrounds offered opinions on an individual case study involving the misapplication of a human resources policy, considering how it may have deviated from lawful practice and the potential impact this had on both the individual and the organisation. Thematic analysis was carried out on this qualitative feedback to identify superordinate and subordinate themes. Results The thematic analysis identified four superordinate themes: failure to follow organisational policies; impact on the individual; impact on the organisation; and failure to learn. Conclusions Poor application of human resources procedures can cause harm to individuals and organisations in a number of different ways. Human resources departments need to actively protect the health and wellbeing of the individual/s involved in investigative procedures, rather than focusing solely on executing the process.
Scanning Tunneling Microscopy of Freeze-Fracture Replicas of Biomembranes (1988)

The high resolution of the scanning tunneling microscope (STM) makes it a potentially important tool for the study of biomaterials. Biological materials can be imaged with the STM by a procedure in which fluid, nonconductive biomaterials are replaced by rigid and highly conductive freeze-fracture replicas. The three-dimensional contours of the ripple phase of dimyristoylphosphatidylcholine bilayers were imaged with unprecedented resolution with commercial STMs and standard freeze-fracture techniques. Details of the ripple amplitude, asymmetry, and configuration unobtainable by electron microscopy or x-ray diffraction can be observed relatively easily with the STM.
Integrating Polymerase Chain Reaction, Valving, and Electrophoresis in a Plastic Device for Bacterial Detection (2003)

An integrated plastic microfluidic device was designed and\nfabricated for bacterial detection and identification. The\ndevice, made from poly(cyclic olefin) with integrated\ngraphite ink electrodes and photopatterned gel domains,\naccomplishes DNA amplification, microfluidic valving,\nsample injection, on-column labeling, and separation.\nPolymerase chain reaction (PCR) is conducted in a\nchannel reactor containing a volume as small as 29 nL;\nthermal cycling utilizes screen-printed graphite ink resistors. In situ gel polymerization was employed to form local\nmicrofluidic valves that minimize convective flow of the\nPCR mixture into other regions. After PCR, amplicons\n(products) are electrokinetically injected through the gel\nvalve, followed by on-chip electrophoretic separation.\nAn intercalating dye is admixed to label the amplicons;\nthey are detected using laser-induced fluorescence. Two\nmodel bacteria, &lt;i&gt;Escherichia coli&lt;/i&gt; O157 and &lt;i&gt;Salmonella\ntyphimurium&lt;/i&gt;, were chosen to demonstrate bacterial\ndetection and identification based on amplification of\nseveral of their unique DNA sequences. The limit of\ndetection is about six copies of target DNA.
Challenges in supporting end-user privacy and security management with social navigation (2009)

Social navigation is a promising approach for supporting privacy and security management. By aggregating and presenting the choices made by others, social navigation systems can provide users with easily understandable guidance on security and privacy decisions, rather than requiring that they understand low-level technical details in order to make informed decisions. We have developed two prototype systems to explore how social navigation can help users manage their privacy and security. The Acumen system employs social navigation to address a common privacy activity, managing Internet cookies, and the Bonfire system uses social navigation to help users manage their personal firewall. Our experiences with Acumen and Bonfire suggest that, despite the promise of social navigation, there are significant challenges in applying these techniques to the domains of end-user privacy and security management. Due to features of these domains, individuals may misuse community data when making decisions, leading to incorrect individual decisions, inaccurate community data, and behavior that is an example of what economists term an informational cascade. By understanding this phenomenon in these terms, we develop and present two general approaches for mitigating herding in social navigation systems that support end-user security and privacy management, mitigation via algorithms and mitigation via user interaction. Mitigation via user interaction is a novel and promising approach to mitigating cascades in social navigation systems.
Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus (2019)

<i>Staphylococcus aureus</i> is a Gram-positive pathogenic bacterium that colonizes an estimated one-third of the human population and can cause a wide spectrum of disease, ranging from superficial skin infections to life-threatening sepsis. The adaptive mechanisms that contribute to the success of this pathogen remain obscure partially due to a lack of knowledge of its metabolic requirements. Systems biology approaches can be extremely useful in predicting and interpreting metabolic phenotypes; however, such approaches rely on a chemically defined minimal medium as a basis to investigate the requirements of the cell. In this study, a chemically defined minimal medium formulation, termed synthetic minimal medium (SMM), was investigated and validated to support growth of three <i>S. aureus</i> strains: LAC and TCH1516 (USA300 lineage), as well as D592 (USA100 lineage). The formulated SMM was used in an adaptive laboratory evolution experiment to probe the various mutational trajectories of all three strains leading to optimized growth capabilities. The evolved strains were phenotypically characterized for their growth rate and antimicrobial susceptibility. Strains were also resequenced to examine the genetic basis for observed changes in phenotype and to design follow-up metabolite supplementation assays. Our results reveal evolutionary trajectories that arose from strain-specific metabolic requirements. SMM and the evolved strains can also serve as important tools to study antibiotic resistance phenotypes of <i>S. aureus</i><b>IMPORTANCE</b> As researchers try to understand and combat the development of antibiotic resistance in pathogens, there is a growing need to thoroughly understand the physiology and metabolism of the microbes. <i>Staphylococcus aureus</i> is a threatening pathogen with increased antibiotic resistance and well-studied virulence mechanisms. However, the adaptive mechanisms used by this pathogen to survive environmental stresses remain unclear, mostly due to the lack of information about its metabolic requirements. Defining the minimal metabolic requirements for <i>S. aureus</i> growth is a first step toward unraveling the mechanisms by which it adapts to metabolic stresses. Here, we present the development of a chemically defined minimal medium supporting growth of three <i>S. aureus</i> strains, and we reveal key genetic mutations contributing to improved growth in minimal medium.
Ineffectiveness of Lactobacillus johnsonii LA1 for prophylaxis of postoperative recurrence in Crohn’s disease: a randomised, double blind, placebo controlled GETAID trial (2005)

L johnsonii LA1 (4 x 10(9) cfu/day) did not have a sufficient effect, if any, to prevent endoscopic recurrence of Crohn's disease.
Finite Difference Time Domain (Fdtd) Analysis of an Artificially-Synthesized Absorbing Medium (2001)

In this paper, we investigate an artificially-synthesized absorbing medium by using the Finite Difference Time Domain (FDTD) technique. The artificial medium is composed of a doubly-periodic array of lossy electric and magnetic material blocks (i.e., μ and ε media arranged in a checkerboard configuration). We analyze its reflection characteristics for both normal and oblique incidence cases. It is demonstrated that, if properly designed, the reflection characteristics of the checkerboard are considerably superior to those of a uniform ε = μ material of the same thickness. A multi-layer checkerboard is used to truncate a waveguide in the FDTD simulation; the result is comparable to that of an unsplit Perfectly Matched Layer (PML) with the same number of layers.
Comparison of an FAP-targeted, CD137 activating DARPin drug candidate with a non-targeted, CD137 activating antibody in a human PBMC transplanted HT-29 mouse tumor model. (2017)

e14626 Background: Urelumab (BMS-663513) is a humanized monoclonal antibody binding to CD137 which, upon Fc-clustering, leads to activation of T-cells. Urelumab is currently in Phase 2 clinical development and has been reported to cause significant hepatotoxicities (around 15% Grade ≥2 ALT and AST elevation) when given as infusion every 3 weeks at doses ≥0.3 mg/kg. Currently ongoing clinical trials report decreased systemic toxicity but limited efficacy at lower doses of urelumab. We hypothesized that more effective triggering of CD137 without associated systemic toxicity may be achieved by targeting a CD137 agonistic engager without Fc to fibroblast activation protein (FAP) which is abundantly expressed in the stroma of many solid tumors. To achieve this, a targeted molecule belonging to the DARPin family of binding proteins was composed of one FAP- and two CD137-binding domains in a “beads on a string” format and tested in a mouse model with human PBMCs. Methods: Human PBMCs were used to reconstitute the immune system in NOG mice implanted subcutaneously with HT-29 human colon cancer cells. Mice were monitored for survival, body weight, and tumor size during the treatment phase of two weeks. Results: None of the mice in the control group died and no significant body weight loss was observed. Six of ten (60%) mice in the CD137 antibody group showed strong signs of graft vs. host disease and either died or reached the termination criterion of ≥20% body weight loss and were sacrificed. One of 30 (3%) mice died in the DARPin drug candidate groups but none of the animals showed body weight loss of ≥20% (p &lt; 0.001, Log-rank test). Tumor growth inhibition was comparable for all treatment groups (around 20-30% at Day 18, p &lt; 0.05 vs. control, Mann Whitney Test). Conclusions: This study confirms the hypothesis that systemic toxicities caused by the urelumab mode of action can be circumvented by FAP-targeting of a CD137 agonistic DARPin drug candidate while achieving comparable tumor growth inhibition. Consequently, higher clinical doses of tumor stroma-targeted agonistic DARPin drug candidates might be possible, and may result in stronger tumor growth inhibition.
The Role of Ru in Improving the Activity of Pd toward Hydrogen Evolution and Oxidation Reactions in Alkaline Solutions (2019)

Improving the reaction kinetics of hydrogen evolution and oxidation reactions (HER/HOR) in alkaline media is critical to promote the development of alkaline fuel cells and electrolyzers. Here, we prepared Pd3Ru alloy nanocatalysts with Ru segregated on the surfaces, forming adatoms and clusters. This structure dramatically lowered the overpotential of Pd toward HER in 1 M KOH by 104 mV at 10 mA cm–2. The HER activity was even higher than that of Pt (6 mV improvement at 10 mA cm–2). Theoretical simulation results revealed that Ru adatoms/clusters on the surface could weaken the hydrogen-binding energy and promote the OH adsorption, consequently lowering the reaction barrier of the rate-determining step in HER. Our findings are of significance for clarifying the role of Ru in bimetallic catalysts and rational design of more active catalysts for HER/HOR.
Joint symbol timing and frequency offset estimation for wireless OFDM systems (2008)

This work presents a new technique for blind and joint estimation of symbol timing and carrier frequency offset in wireless orthogonal frequency division multiplexing (OFDM) systems. The joint estimation is achieved by sensing the interference introduced at the fast Fourier transform (FFT) output when a carrier frequency or timing offsets exist. The synchronization parameters are selected such that the interference is minimized. The proposed joint estimator is highly efficient because it does not require any overhead or channel state information. Simulation results show that the system is effective and robust even at low signal-to-noise ratios.
Astrocyte‐intrinsic regulation of central nervous system inflammation and neurodegeneration (2016)

Abstract Astrocytes constitute the majority of cells in the mammalian brain, where they carry out fine‐tuned tasks that include, for example, the formation of the blood–brain barrier, the provision of structural support, the regulation of ion homeostasis and neurotransmitter recycling, and the modulation of neuronal function. In the context of autoimmune inflammation in the central nervous system during multiple sclerosis, these and other functions are challenged, while astrocytes modulate the local inflammatory response not only by regulating the blood–brain barrier permeability, but also by controlling the recruitment and activation of inflammatory cells and neurotoxicity. In the present review, we discuss astrocyte‐intrinsic mechanisms that affect multiple sclerosis pathology and might provide potential targets for therapeutic intervention.
Collective coordinate control of density distributions (2006)

Real collective density variables C(k) [cf. Eq. 1 3 ] in many-particle systems arise from nonlinear transformations of particle positions, and determine the structure factor S(k) , where k denotes the wave vector. Our objective is to prescribe C(k) and then to find many-particle configurations that correspond to such a target C(k) using a numerical optimization technique. Numerical results reported here extend earlier one- and two-dimensional studies to include three dimensions. In addition, they demonstrate the capacity to control S(k) in the neighborhood of |k|=0. The optimization method employed generates multiparticle configurations for which S(k) proportional, |k|alpha, |k|<or=K, and alpha=1, 2, 4, 6, 8, and 10. The case alpha=1 is relevant for the Harrison-Zeldovich model of the early universe, for superfluid 4He, and for jammed amorphous sphere packings. The analysis also provides specific examples of interaction potentials whose classical ground states are configurationally degenerate and disordered.
A New Cyclic Phosphoramidate D4T Prodrug ApproachcycloAmb-D4T-Phosphoramidates (1999)

A new potential phosphoramidate prodrug approach for d4T 1 is described. In hydrolyses studies the cycloAmb-d4T-phosphoramidates 2 and 3 proved to deliver d4TMP following a tandem reaction.
A concept of a novel edge termination technique: Junction termination (RJT) (2010)

This paper presents a novel junction termination technique, named Recess Junction Termination (RJT), for power devices. This new junction termination improves the breakdown voltage of a planar junction by a silicon recess located to create a positive bevel, which reduces the peak of electric field. The RJT can reduce a thermal budget for the RESURF (REduced SURface Field) layer by the silicon recess, and has compatibility with a fine-pitch process due to a planarization process using Chemical Mechanical Polish (CMP) treatments. After numerous simulations to optimize the structure parameters, we have succeeded in obtaining sufficient blocking capabilities of pn-RJT-diodes, the voltage ratings of which are from 75 V to 1700 V.
Modeling Touch Point Distribution with Rotational Dual Gaussian Model (2021)

Touch point distribution models are important tools for designing touchscreen interfaces. In this paper, we investigate how the finger movement direction affects the touch point distribution, and how to account for it in modeling. We propose the Rotational Dual Gaussian model, a refinement and generalization of the Dual Gaussian model, to account for the finger movement direction in predicting touch point distribution. In this model, the major axis of the prediction ellipse of the touch point distribution is along the finger movement direction, and the minor axis is perpendicular to the finger movement direction. We also propose using <i>projected</i> target width and height, in lieu of nominal target width and height to model touch point distribution. Evaluation on three empirical datasets shows that the new model reflects the observation that the touch point distribution is elongated along the finger movement direction, and outperforms the original Dual Gaussian Model in all prediction tests. Compared with the original Dual Gaussian model, the Rotational Dual Gaussian model reduces the RMSE of touch error rate prediction from 8.49% to 4.95%, and more accurately predicts the touch point distribution in target acquisition. Using the Rotational Dual Gaussian model can also improve the soft keyboard decoding accuracy on smartwatches.
Slow light enhanced sensitivity of resonance modes in photonic crystal biosensors (2013)

We demonstrate experimentally that in photonic crystal sensors with a side-coupled cavity-waveguide configuration, group velocity of the propagating mode in the coupled waveguide at the frequency of the resonant mode plays an important role in enhancing the sensitivity. In linear L13 photonic crystal microcavities, with nearly same resonance mode quality factors ∼7000 in silicon-on-insulator devices, sensitivity increased from 57 nm/RIU to 66 nm/RIU as group index in the coupled waveguide increased from 10.2 to 13.2. Engineering for highest sensitivity in such planar integrated sensors, thus, requires careful slow light design for optimized sensor sensitivity.
Aryl-imidazothiadiazole analogues as microtubule disrupting agents (2015)

Disruption of tubulin polymerization and the docked pose of<bold>5k</bold>in the colchicine binding site of tubulin.
Discovery and characterization of thermophilic limonene‐1,2‐epoxide hydrolases from hot spring metagenomic libraries (2015)

The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides and 1,2-diols which are valuable building blocks for the synthesis of several pharmaceutical compounds. A metagenomic approach has been used to identify two new members of the atypical EH limonene-1,2-epoxide hydrolase (LEH) family of enzymes. These two LEHs (Tomsk-LEH and CH55-LEH) show EH activities towards different epoxide substrates, differing in most cases from those previously identified for Rhodococcus erythropolis (Re-LEH) in terms of stereoselectivity. Tomsk-LEH and CH55-LEH, both from thermophilic sources, have higher optimal temperatures and apparent melting temperatures than Re-LEH. The new LEH enzymes have been crystallized and their structures solved to high resolution in the native form and in complex with the inhibitor valpromide for Tomsk-LEH and poly(ethylene glycol) for CH55-LEH. The structural analysis has provided insights into the LEH mechanism, substrate specificity and stereoselectivity of these new LEH enzymes, which has been supported by mutagenesis studies.
Frangi-Net: A Neural Network Approach to Vessel Segmentation (2017)

In this paper, we reformulate the conventional 2-D Frangi vesselness measure into a pre-weighted neural network ("Frangi-Net"), and illustrate that the Frangi-Net is equivalent to the original Frangi filter. Furthermore, we show that, as a neural network, Frangi-Net is trainable. We evaluate the proposed method on a set of 45 high resolution fundus images. After fine-tuning, we observe both qualitative and quantitative improvements in the segmentation quality compared to the original Frangi measure, with an increase up to $17\%$ in F1 score.
Training less-experienced faculty improves reliability of skills assessment in cardiac surgery (2021)

OBJECTIVE: Previous work has demonstrated high inter-rater reliability in the objective assessment of simulated anastomoses among experienced educators. We evaluated the inter-rater reliability of less-experienced educators and the impact of focused training with a video-embedded coronary anastomosis assessment tool. METHODS: Nine less-experienced cardiothoracic surgery faculty members from different institutions evaluated 2 videos of simulated coronary anastomoses (1 by a medical student and 1 by a resident) at the Thoracic Surgery Directors Association Boot Camp. They then underwent a 30-minute training session using an assessment tool with embedded videos to anchor rating scores for 10 components of coronary artery anastomosis. Afterward, they evaluated 2 videos of a different student and resident performing the task. Components were scored on a 1 to 5 Likert scale, yielding an average composite score. Inter-rater reliabilities of component and composite scores were assessed using intraclass correlation coefficients (ICCs) and overall pass/fail ratings with kappa. RESULTS: All components of the assessment tool exhibited improvement in reliability, with 4 (bite, needle holder use, needle angles, and hand mechanics) improving the most from poor (ICC range, 0.09-0.48) to strong (ICC range, 0.80-0.90) agreement. After training, inter-rater reliabilities for composite scores improved from moderate (ICC, 0.76) to strong (ICC, 0.90) agreement, and for overall pass/fail ratings, from poor (kappa = 0.20) to moderate (kappa = 0.78) agreement. CONCLUSIONS: Focused, video-based anchor training facilitates greater inter-rater reliability in the objective assessment of simulated coronary anastomoses. Among raters with less teaching experience, such training may be needed before objective evaluation of technical skills.
New paradigms for approximate nearest-neighbor search (2013)

Nearest-neighbor search is a very natural and universal problem in computer science. Often times, the problem size necessitates approximation. In this thesis, I present new paradigms for nearest-neighbor search (along with new algorithms and theory in these paradigms) that make nearest-neighbor search more usable and accurate. First, I consider a new notion of search error, the rank error, for an approximate neighbor candidate. Rank error corresponds to the number of possible candidates which are better than the approximate neighbor candidate. I motivate this notion of error and present new efficient algorithms that return approximate neighbors with rank error no more than a user specified amount. Then I focus on approximate search in a scenario where the user does not specify the tolerable search error (error constraint); instead the user specifies the amount of time available for search (time constraint). After differentiating between these two scenarios, I present some simple algorithms for time constrained search with provable performance guarantees. I use this theory to motivate a new space-partitioning data structure, the max-margin tree, for improved search performance in the time constrained setting. Finally, I consider the scenario where we do not require our objects to have an explicit fixed-length representation (vector data). This allows us to search with a large class of objects which include images, documents, graphs, strings, time series and natural language. For nearest-neighbor search in this general setting, I present a provably fast novel exact search algorithm. I also discuss the empirical performance of all the presented algorithms on real data.
Modified Smith Predictor Scheme for Periodic Disturbances Reduction in the Continuous Casting Process (2009)

International audience