gebhart/patrepeval huggingface dataset:
S0861 Comparative Risk of Serious Infections With Tumor Necrosis Factor-α Antagonists vs Vedolizumab in Patients With Inflammatory Bowel Diseases (2020)

INTRODUCTION: Comparative safety of therapies is an important attribute in choosing optimal therapy in patients with inflammatory bowel diseases (IBD). We conducted a retrospective cohort study comparing the risk of serious infections between patients treated with tumor necrosis factor-α (TNFα) antagonists and those treated with vedolizumab. METHODS: Using an administrative claims database (OptumLabs Data Warehouse) we identified patients with IBD who were new-users of either TNFα antagonists or vedolizumab between 2014 and 2019 and had insurance coverage for at least 1y before and 1y after treatment initiation. We compared the risk of serious infections between patients treated with TNFα antagonists and those treated with vedolizumab using marginal structural Cox proportional hazard models adjusted for ulcerative colitis (UC) versus Crohn’s disease (CD), baseline demographics, healthcare utilization, comorbidities and time-varying use of IBD-related medications including corticosteroids and immunomodulators. RESULTS: We included 4896 patients treated with TNFα antagonists (age, 41 ± 15 y, 51% male, 60% with CD) of whom 434 developed serious infections over a 6009 person-year [py] follow-up, and 1106 patients treated with vedolizumab (age, 44 ± 16 y, 49% male, 39% with CD) of whom 86 developed serious infections over a 1077 py follow-up. On adjusted analysis, TNFα antagonists were associated with 2.4-fold higher risk of serious infections (hazard ratio [HR], 2.38 [95% CI, 1.38–4.13]) when compared with vedolizumab in all patients with IBD, and in subgroup analyses of patients with CD (HR, 2.28 [1.13–4.62]) and UC (HR, 1.62 [1.03–2.5]). This was primarily driven by increased risk of extra-intestinal serious infections (HR, 3.13 [1.48–6.63]), without any increase in risk of serious gastrointestinal infections (HR, 0.60 [0.33–1.08]). CONCLUSION: In a large claims-based study, TNFα antagonists were associated with increased risk of serious infections as compared with vedolizumab, in patients with CD and UC, particularly risk of extra-intestinal infections.
Assessment of left ventricular myocardial scar in coronary artery disease by a three-dimensional MR imaging technique (2012)

Free-breathing 3D PSIR Turbo FLASH imaging is another feasible method to identify left ventricular myocardial scar in patients with CAD and detects more scar volume compared with breathhold 2D PSIR Turbo FLASH imaging.
Electrical treeing in polyethylene-alumina-filled nanocomposites for HVDC applications (2015)

Electrical tree formations under DC pre-stress followed by an application of voltage pulses of opposite polarities were observed in low density polyethylene and its nanocomposite filled with 1.0 wt% and 3.0 wt% alumina nanoparticles. A special wire-plane electrode geometry were manufactured for the test. The obtained experimental results indicate that the addition of the nanoparticles has a positive impact on the resistance to electrical treeing. In addition to the reported above results, a thermal ageing and electro-thermal experiment is presently being conducted and the results comparing the treeing behavior after it will also be presented.
Directivity and Frequency-Dependent Effective Sensitive Element Size of Needle Hydrophones: Predictions From Four Theoretical Forms Compared With Measurements (2018)

Directivity is a hydrophone specification that describes response as a function of angle of incidence. The goal of this study was to compare, in the context of needle hydrophones, the commonly used rigid baffle model for hydrophone directivity to three alternative models: soft baffle, unbaffled (UB), and rigid piston (RP). Directivity measurements were performed at 1, 2, 3, 4, 6, 8, and 10 MHz from ±7° in two orthogonal planes for two ceramic and two polymer needle hydrophones with nominal geometrical sensitive element diameters of 200, 400, 600, and 1000 . Effective hydrophone sensitive element radius was estimated by least-squares fitting the four models to directivity measurement data using the sensitive element radius (a) as an adjustable parameter. For > 4 (where and = wavelength), the RP model outperformed the other three models. For , the average error in estimated sensitive element radius was 7% [95% confidence interval (CI): 3%-12%] for the RP model while the lowest average error by the other three models was 46% (95% CI: 38%-54%) for the UB model.
Systematic evaluation of non-animal test methods for skin sensitisation safety assessment (2014)

The need for non-animal data to assess skin sensitisation properties of substances, especially cosmetics ingredients, has spawned the development of many in vitro methods. As it is widely believed that no single method can provide a solution, the Cosmetics Europe Skin Tolerance Task Force has defined a three-phase framework for the development of a non-animal testing strategy for skin sensitization potency prediction. The results of the first phase – systematic evaluation of 16 test methods – are presented here. This evaluation involved generation of data on a common set of ten substances in all methods and systematic collation of information including the level of standardisation, existing test data,potential for throughput, transferability and accessibility in cooperation with the test method developers.A workshop was held with the test method developers to review the outcome of this evaluation and to discuss the results. The evaluation informed the prioritisation of test methods for the next phase of the non-animal testing strategy development framework. Ultimately, the testing strategy – combined with bioavailability and skin metabolism data and exposure consideration – is envisaged to allow establishment of a data integration approach for skin sensitisation safety assessment of cosmetic ingredients.
Supplemental Figure 2 (2015)

Number of SNPs retained by UNEAK and PoPoolation2 pipelines at different parameter values on an ApeKI library from 23 worldwide populations of Globodera rostochiensis. ‘MAF’ is the minimum allele frequency; ‘minCov’ is the minimum number of reads/locus/population required to accept a SNP; ‘mnC’ is the minimum proportion of populations in which a locus must have been scored to be accepted. PoPoolation2 does not allow missing data (mnC = 1.0). *The number of SNPs identified by UNEAK was not influenced by the ‘mnC’ value when the minimum allele frequency was set to 5% (MAF = 0.05).
Chemically Tuning the Antigen Release Kinetics from Spherical Nucleic Acids Maximizes Immune Stimulation (2021)

Cancer vaccine structure is emerging as an important design factor that offers tunable parameters to enhance the targeted immune response. We report the impact of altering the antigen release rate from spherical nucleic acid (SNA) vaccines-nanoparticles with a liposomal core and surface-anchored adjuvant DNA-on immune stimulation. Peptide antigens were incorporated into SNAs using either a nonreducible linker or one of a series of reduction-triggered traceless linkers that release the native peptide at rates controlled by their substitution pattern. Compared with a nonreducible linkage, the traceless attachment of antigens resulted in lower EC<sub>50</sub> of T cell proliferation <i>in vitro</i> and greater dendritic cell (DC) activation and higher T cell killing ability <i>in vivo</i>. Traceless linker fragmentation rates affected the rates of antigen presentation by DCs and were correlated with the <i>in vitro</i> potencies of SNAs. Antigen release was correlated with the <i>ex vivo</i> -log(EC<sub>50</sub>), and more rapid antigen release resulted in an order of magnitude improvement in the EC<sub>50</sub> and earlier and greater antigen presentation over the same time-period. <i>In vivo</i>, increasing the rate of antigen release resulted in higher T cell activation and target killing. These findings provide fundamental insights into and underscore the importance of vaccine structure.
GalNAc-siRNA Conjugates: Leading the Way for Delivery of RNAi Therapeutics (2018)

Short-interfering RNA (siRNA)-induced RNAi responses have great potential to treat a wide variety of human diseases from cancer to pandemic viral outbreaks to Parkinson's Disease. However, before siRNAs can become drugs, they must overcome a billion years of evolutionary defenses designed to keep invading RNAs on the outside cells from getting to the inside of cells. Not surprisingly, significant effort has been placed in developing a wide array of delivery technologies. Foremost of these has been the development of N-acetylgalactosamine (GalNAc) siRNA conjugates for delivery to liver. Tris-GalNAc binds to the Asialoglycoprotein receptor that is highly expressed on hepatocytes resulting in rapid endocytosis. While the exact mechanism of escape across the endosomal lipid bilayer membrane remains unknown, sufficient amounts of siRNAs enter the cytoplasm to induce robust, target selective RNAi responses in vivo. Multiple GalNAc-siRNA conjugate clinical trials, including two phase III trials, are currently underway by three biotech companies to treat a wide variety of diseases. GalNAc-siRNA conjugates are a simple solution to the siRNA delivery problem for liver hepatocytes and have shown the RNAi (and antisense oligonucleotide) field the path forward for targeting other tissue types.
The effect of Er211 additions on the microstructure and magnetic properties of zone-melt textured Y123 (1994)

YBa2Cu3O6+x(Y123) wires with Er2BaCuO5 (Er211) and Y2BaCuO5 (Y211) additions were textured by a zone-melting process. The microstructure and magnetic Jc of wire segments taken from different sections of textured wires were analysed and compared. Microstructural analysis on the Er211-doped wires confirms that Er211 dissolves in the melt and results in the formation of a YzEr(1-z)Ba2Cu3O6+x superconducting phase upon solidification which shows improved magnetic properties over Y211 doped wires.
Opportunities via extended networks for teens' informal learning (2013)

With the increasing use of the Internet and social media for knowledge and social connections, we might expect that people more easily expand their opportunities for new learning through social relationships online. Yet, this mixed methods study of teens' use of technologies (e.g. YouTube and social media) in informal learning contexts reveals that, in teens' preferred learning activities, few interact with new ties outside their immediate networks (school, family, and friends). Given the value of social interaction and weak ties for learning new knowledge, this research investigates teens' use of networked technologies with people and resources outside their immediate networks. Based on 23 semi-structured interviews, we describe teens' informal learning activities and technology practices, from which we identify design opportunities. To inform these, we examine teens' paths into extended networks, including the role of digital skills, technology access, intrinsic motivation, and sense of relatedness. We find that relatedness both motivated and inhibited teens to reach beyond immediate networks into extended networks for informal learning activities.
Adaptive Optics Performance Over Long Horizontal Paths: Aperture Effects in Multi-Conjugate Adaptive Optical Systems (2007)

We analyze various scenarios of the aperture effects in adaptive optical receiver-type systems when inhomogeneities of the wave propagation medium are distributed over long horizontal propagation path, or localized in a few thin layers remotely located from the receiver telescope pupil. Phase aberration compensation is performed using closed-loop control architectures based on phase conjugation and decoupled stochastic parallel gradient descent (DSPGD) control algorithms. Both receiver system aperture diffraction effects and the impact of wavefront corrector position on phase aberration compensation efficiency are analyzed for adaptive systems with single or multiple wavefront correctors.
Morphologic Variations of the Umbilical Ring, Umbilical Ligaments and Ligamentum Teres Hepatis (2008)

These results are expected to improve our understanding of the anatomy of the umbilical area, and further improve treatments of the umbilical hernia.
Evaluating the 4‐hour and 30‐minute rules: effects of room temperature exposure on red blood cell quality and bacterial growth (2012)

Single or multiple RT exposures did not affect RBC quality but slightly promoted bacterial growth in contaminated units. The clinical significance of these results remains unclear and needs further investigation.
CHD2 haploinsufficiency is associated with developmental delay, intellectual disability, epilepsy and neurobehavioural problems (2014)

The results of this study, in addition to our review of the literature, support a causative role of CHD2 haploinsufficiency in developmental delay, intellectual disability, epilepsy and behavioural problems, with phenotypic variability between individuals.
Identification of Candidate Mitochondrial Inheritance Determinants Using the Mammalian Cell-Free System (2023)

Abstract The degradation of sperm-borne mitochondria after fertilization is a conserved event. This process known as post-fertilization sperm mitophagy, ensures exclusively maternal inheritance of the mitochondria-harbored mitochondrial DNA genome. This mitochondrial degradation is in part carried out by the ubiquitin proteasome system. In mammals, ubiquitin-binding pro-autophagic receptors such as SQSTM1 and GABARAP have also been shown to contribute to sperm mitophagy. These systems work in concert to ensure the timely degradation of the sperm-borne mitochondria after fertilization. We hypothesize that other receptors, cofactors, and substrates are involved in post-fertilization mitophagy. Mass spectrometry was used in conjunction with a porcine cell-free system to identify other autophagic cofactors involved in post-fertilization sperm mitophagy. This porcine cell-free system is able to recapitulate early fertilization proteomic interactions. Altogether, 185 proteins were identified as statistically different between control and cell-free treated spermatozoa. Six of these proteins were further investigated, including MVP, PSMG2, PSMA3, FUNDC2, SAMM50, and BAG5. These proteins were phenotyped using porcine in vitro fertilization, cell imaging, proteomics, and the porcine cell-free system. The present data confirms the involvement of known mitophagy determinants in the regulation of mitochondrial inheritance and provides a master list of candidate mitophagy co-factors to validate in the future hypothesis-driven studies.
Biomechanical Considerations for Child Occupant Protection (1998)

This paper discusses the differences in injury patterns between adults and children under similar loading conditions during an automotive crash event. Because of the recent awareness and the ensuing necessity, as an example, injuries including fatalities due to airbag deployment are discussed. Biomechanical differences explain the varying injury patterns and mechanisms of injury. The commonly adopted scaling techniques for predicting pediatric tolerances are described. A comparison of the biomechanical properties of the pediatric and adult structures is given. Some insight is provided with regard to the use of these data to develop validated mathematical models of pediatric structures. The paper concludes with recommendations for further research.
Faculty Opinions recommendation of Genetic variation in glutathione metabolism and DNA repair genes predicts survival of small-cell lung cancer patients. (2010)

Background: Small-cell lung cancer (SCLC) carries the worst prognosis among lung cancer diagnoses. Combined radiation and chemotherapy is the standard of care; however, treatment outcomes vary. Variability in the rate at which chemotherapy agents are metabolized and in the capacity of repairing DNA damage has been hypothesized to be partly responsible for the treatment response variation. Genes in the glutathione metabolism and DNA repair pathways were tested through tag single-nucleotide polymorphisms (SNPs) to assess their association with survival in SCLC.
Enhanced Particle Swarm Optimization-Based Feeder Reconfiguration Considering Uncertain Large Photovoltaic Powers and Demands (2014)

The Kyoto protocol recommended that industrialized countries limit their green gas emissions in 2012 to 5.2% below 1990 levels. Photovoltaic (PV) arrays provide clear and sustainable renewable energy to electric power systems. Solar PV arrays can be installed in distribution systems of rural and urban areas, as opposed to wind-turbine generators, which cause noise in surrounding environments. However, a large PV array (several MW) may incur several operation problems, for example, low power quality and reverse power. This work presents a novel method to reconfigure the distribution feeders in order to prevent the injection of reverse power into a substation connected to the transmission level. Moreover, a two-stage algorithm is developed, in which the uncertain bus loads and PV powers are clustered by fuzzy-c-means to gain representative scenarios; optimal reconfiguration is then achieved by a novel mean-variance-based particle swarm optimization. The system loss is minimized while the operational constraints, including reverse power and voltage variation, are satisfied due to the optimal feeder reconfiguration. Simulation results obtained from a 70-bus distribution system with 4 large PV arrays validate the proposed method.
Potential of an Indigenous Fungus, Plectosporium tabacinum, as a Mycoherbicide for Control of Arrowhead (Sagittaria trifolia) (1998)

An isolate of the indigenous fungus Plectosporium tabacinum was isolated from arrowhead (Sagittaria trifolia) in Yusung, Korea in 1990 and evaluated in laboratory and growth chamber tests as a potential mycoherbicide. The fungus grew comparatively slowly on potato dextrose agar and corn meal agar, attaining a diameter of 65 mm after 12 days at 25°C. Conidia were mass-produced in shake-cultures or in a fermentor using potato dextrose broth containing yeast extract (0.5%, wt/vol) at 25°C. When arrowhead seedlings at the 2- to 3-leaf stage were inoculated with conidial suspensions (2 × 10<sup>7</sup> conidia/ml) and incubated in a dew chamber for 18 h at 25°C, the plants developed small, brown spots on the leaves and petioles in 2 days, and were blighted completely within 7 days after inoculation. This effect was consistent on arrowhead plants from the 2- to 5-leaf stage. Another arrowhead species, S. pygmaea, was as susceptible as S. trifolia to the pathogen. Several crops, including rice, barley, and wheat and 34 other common weed species, were immune. In small-scale field tests in paddy fields during the summers of 1992 and 1993, a mean reduction of 71.3% in the number of arrowhead plants was observed following a foliar spray of a conidial suspension (10<sup>7</sup> conidia/ml). These results indicate that P. tabacinum has potential as a selective mycoherbicide for arrowhead control.
Challenges in the Operation and Design of Intelligent Cyber‐Physical Systems (2019)

As technology advances unleash ubiquitous access to inexpensive and highly powerful means for computation, cyber-physical systems are increasingly becoming an integral part of real-world applications such as manufacturing and consumer electronics. With sophisticated computational functionality implemented as software, these systems are rapidly becoming intelligent and autonomous. Advances in low latency and high throughput reliable communication are enabling such autonomous systems to be networked and interconnected for collaborative operation. The new and evolving capabilities of autonomous and connected engineering systems mean that these intelligent cyber-physical systems are becoming more complex and therefore more challenging to design, test, and operate. This chapter introduces a classification of intelligent cyber-physical systems along two key axes: the behavior dimension launched by the advances in computation, which corresponds to the degree of autonomy in the systems, and the configuration dimension catalyzed by the advances in communication, which refers to the scale of the system in terms of the number of connected elements that comprise it. Based on this classification, the chapter explores practical challenges that may arise throughout the design-test-operation lifecycle of such systems and outlines the various ways in which computational models can provide value in addressing those challenges.
Identification of Indirubin as a metabolite of Malassezia furfur strains isolated from diseased skin (2008)

Seborrheic dermatitis (SD), pityriasis versicolor (PV) and dandruff (DF) are common skin diseases that are unequivocally associated with Malassezia yeasts. In a previous work [1] we compared M. furfur isolates from healthy and SD skin for the production of indole derivatives, using HPLC-UV and identified the preferential biosynthesis of several known indole derivatives [2,3] such as malassezin, pityriacitrin, malassezindol A, indol-3-carboxaldehyde, indolo[3,2-b]carbazol (ICZ) by M. furfur strains isolated from diseased skin. Further investigation of ethyl acetate extracts of M. furfur strains grown on L-tryptophan agar originating from SD, PV and DF, using preparative HPLC, led to -in addition to the aforementioned indoles- the isolation and structure elucidation by NMR and MS of indirubin. Indirubin which is a known highly potent ligand of the Aryl hydrocarbon receptor (AhR) and a strong inhibitor of several protein kinases is described for the first time as a metabolite of M.furfur. Isolated indirubin was used as standard for the development of an analytic methodology using HPLC-DAD. HPLC analysis of the extracts coming from 15 reference and clinical strains (7 healthy, 8 disease) revealed the preferential in vitro production of indirubin only by M. furfur strains isolated from skin lesions and not healthy skin controls. The selective production of compounds like ICZ and indirubin which are active AhR ligands offers indirect, statistical significant evidence in favor of the variable pathogenic potential within M. furfur strains as well as the possible implication of AhR activation in the pathogenesis of PV, SD and DF. In addition, the common facial distribution of SD and basal cell carcinoma, coupled by the inhibitory effect of indirubin on the GSK-3 enzyme – a Hedgehog pathway implicated enzyme – are suggestive of the potential implication of Malassezia metabolites in the development of non-melanoma skin cancer.