gebhart/patrepeval huggingface dataset:
Rationale for Using Social Media to Collect Patient-Reported Outcomes in Patients with Celiac Disease (2014)

Patients with celiac disease (CD) are increasingly interconnected through social media, exchanging patient experiences and health-tracking information between individuals through various web-based platforms. Social media represents potentially unique communication interface between gastroenterologists and active social media users - especially young adults and adolescents with celiac disease-regarding adherence to the strict gluten-free diet, gastrointestinal symptoms, and meaningful discussion about disease management. Yet, various social media platforms may be underutilized for research purposes to collect patient-reported outcomes data. In this commentary, we summarize the scientific rationale and potential for future growth of social media in patient-reported outcomes research, focusing on college freshmen with celiac disease as a case study and provide overview of the methodological approach. Finally, we discuss how social media may impact patient care in the future through increasing mobile technology use.
WIPP/SRL international in situ testing program: MIIT (Materials Interface Interactions Tests) (1988)

On July 22, 1986, the largest and most cooperative international effort directed at in situ testing of simulated waste glasses was officially begun. This program, called the Materials Interface Interactions Tests (MIIT), involves the underground emplacement of almost 2000 simulated HLW samples, package components, and eologic samples in the bedded salt site at the Waste Isolation Plant (WIPP), near Carlsbad, New Mexico. Samples were supplied by researchers in the United States, France, Germany, Canada, Belgium, Japan, and the United Kingdom. Data and sample performance are being assessed and analyzed by laboratories and universities in each of the participating countries and additional nations also. Samples have been retrieved after 0.5, 1, and 2 years of burial with only the 5 year samples still in test. There are hundreds of samples available for study and many analyses are currently in progress. At present, even though only a small portion of all the data available has been obtained and analyzed, important effects and trends are already emerging. An overview of the MIIT will be presented along with a summary of preliminary findings on performance of Savannah River (SR) waste glass in the WIPP MIIT. 20 refs., 8 figs.
Methylation-Specific Polymerase Chain Reaction (2005)

Methylation-specific polymerase chain reaction (MSP) is a method that can rapidly assess the methylation status of virtually any group of CpG sites within a CpG island, independent of the use of methylation-sensitive restriction enzymes. This assay entails the initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracils but leaving the methylated cytosines unchanged, followed by subsequent amplification with primers specific for methylated vs unmethylated DNA. The great sensitivity of this technique allows qualitative methylation analysis from DNA obtained not only from fresh frozen tissues, peripheral blood, bone marrow, or body fluids but also from paraffin-embedded samples. It is a rapid and cost-effective method that does not require radioactive reagents and can be used for the analysis of a large number of clinical samples.
Severe Tuberculosis Induces Unbalanced Up‐Regulation of Gene Networks and Overexpression ofIL‐22, MIP‐1α, CCL27, IP‐10, CCR4, CCR5, CXCR3, PD1, PDL2, IL‐3, IFN‐β, TIM1,andTLR2but Low Antigen‐Specific Cellular Responses (2008)

The immune mechanisms by which early host-mycobacterium interaction leads to the development of severe tuberculosis (TB) remain poorly characterized in humans. Here, we demonstrate that severe TB in juvenile rhesus monkeys down-regulated many genes in the blood but up-regulated selected genes constituting gene networks of Th17 and Th1 responses, T cell activation and migration, and inflammation and chemoattractants in the pulmonary and lymphoid compartments. Overexpression (450-2740-fold) of 13 genes encoding inflammatory cytokines and receptors (IL-22, CCL27, MIP-1alpha, IP-10, CCR4, CCR5, and CXCR3), immune dysfunctional receptors and ligands (PD1 and PDL2), and immune activation elements (IL-3, IFN-beta, TIM1, and TLR2) was seen in tissues, with low antigen-specific cellular responses. Thus, severe TB in macaques features unbalanced up-regulation of immune-gene networks without proportional increases in antigen-specific cellular responses.
Adherence of Streptococcus pneumoniae to Human Bronchial Epithelial Cells (BEAS-2B) (1998)

Pneumococcal adherence to alveolar epithelial cells and nasopharyngeal epithelial cells has been well characterized. However, the interaction of Streptococcus pneumoniae with bronchial epithelial cells has not been studied. We have now shown that pneumococci bind specifically to a human bronchial epithelial cell line (BEAS-2B cells). Pneumococci adhered to BEAS-2B cells in a time- and dose-dependent manner. These results suggest that the bronchial epithelium may serve as an additional site of attachment for pneumococci and demonstrate the utility of the BEAS-2B cell line for studying mechanisms of pneumococcal infection.
Mastering the Information Age Solving Problems with Visual Analytics (2022)

Today, in many spheres of human activity, massive amounts of data are collected and stored. As the volumes of data available to lawmakers, civil servants, business people and scientists increase, their effective use becomes more challenging. Simply keeping up to date with the flood of data, using standard tools for data management and analysis, is fraught with difficulty. The field of visual analytics seeks to provide people with better and more effective means to understand and analyse massive amounts of data. It also seeks to enable them to act upon their findings immediately, that is, in real time. Visual analytics integrates the analytic capabilities of the computer and the abilities of the human analyst. In so doing it allows novel discoveries and empowers individuals to take control of the analytical process. Visual analytics opens the door to the discoveries and unexpected insights which lead to beneficial and profitable innovation. This book is the result of the VisMaster project, a coordination action funded by the European Commission to form a strong visual analytics research community.
INFLUÊNCIA DO GRAU DE HIDROFOBICIDADE DE SUPORTES POLIMÉRICOS COM MORFOLOGIA CASCA-NÚCLEO NA IMOBILIZAÇÃO DA LIPASE B DE Candida antarctica(CAL-B) (2015)

RESUMO – O emprego de enzimas na forma imobilizada tem crescido nos ultimos anos, em funcao, principalmente, da possibilidade de reutilizacao de tais enzimas. Dessa forma, objetivando desenvolver biocatalisadores mais eficientes, particulas polimericas com morfologia casca-nucleo, apresentando diferentes graus de hidrofobicidade na casca, foram sintetizadas. Em uma etapa seguinte,tais particulas foram empregadas como suporte na imobilizacao da lipase B de Candida antarctica(CAL-B). Observou-se, entao, que ao alterar a composicao da casca durante a polimerizacao eram obtidas particulas com diferentes polaridades. Notou-se tambem que os biocatalisadores apresentaram maiores atividades de esterificacao, quando suportes com maior carater hidrofobico foram empregados no processo de imobilizacao; possivelmente, em decorrencia da maior exposicao do sitio ativo das enzimas. No entanto, ao analisar as atividades de hidrolise dos biocatalisadores, percebeu-se tambem um aumento de atividade enzimatica quando suportes mais hidrofilicos foram empregados, indicando a presenca de limitacoes difusionais neste tipo de reacao. Percebeu-se, assim, que o desempenho dos biocatalisadoresproduzidos dependenao somente das caracteristicas dos suportes empregados no processo de imobilizacao, mas tambem do meio reacional onde o biocatalisador e empregado.
Discovery and Development of Omecamtiv Mecarbil: A Novel Cardiac Myosin Activator for the Potential Treatment of Systolic Heart Failure (2020)

Omecamtiv mecarbil is a first-in-class, direct activator of cardiac myosin, the motor protein of the cardiac sarcomere that transfers chemical energy (ATP hydrolysis) into a mechanical force for contraction. By promoting the force-generating cycle of myosin, the drug acts like “more hands on the rope” to improve cardiac contractility without increasing cardiac myocyte intracellular calcium concentrations. It is currently being evaluated as a potential treatment for heart failure with the goal of establishing a new continuum of care for patients in both in-hospital and outpatient settings. The first part of this chapter will describe the discovery and candidate selection of omecamtiv mecarbil, including the initial synthetic pathway and the development of an early stage manufacturing process which allowed for rapid advancement in Phase 1/2 clinical evaluation. The second part of the chapter will describe the design of the robust synthetic process used to prepare omecamtiv mecarbil for Phase 3 clinical trials and highlight the challenges and opportunities at the drug substance/drug product interface. This includes optimization of a convergent synthesis of omecamtiv mecarbil’s unsymmetrical urea core from stable precursors, as well as engineering the drug substance particle properties to aid drug product manufacturability and performance.
ICCAD-2013 CAD contest in mask optimization and benchmark suite (2013)

Optical microlithography is the technique of printing a set of shapes on a wafer using light transmitted through a template called a mask. Repeatedly printing and stacking such shapes on top of each other to build electrical circuits allows us to manufacture chips in high volume. However this technique has now reached its fundamental physical limits of resolution. Current 193nm wavelength light is no longer sufficient to reliably transfer patterns which are now in the sub-100nm dimensional range. This has led to increased research in optimizing lithographic masks to pre-compensate for distortions introduced by the lithographic process. This is called mask optimization. In this contest, students are provided with a sample lithographic model which simulates the transfer of a mask pattern on to wafer. The mask is assumed to be a pixelated template, where every pixel can be turned on or off, to indicate where light passes through, or is blocked. Contestants are also provided with models to predict the robustness of their pattern i.e. how much variability is in the transferred pattern. Given these tools, the objective is to minimize the variability in the wafer image, as measured by process variability (PV) bands. This is subject to the constraints of runtime and satisfying pattern fidelity i.e. the transferred pattern should resemble the target pattern. Benchmarks are provided in the form of collections of geometric shapes, each of which provides a challenge in printing at sub-wavelength.
Guidelines for Choosing Compositional and Black-Oil Models for Volatile Oil and Gas-Condensate Reservoirs (2000)

Abstract This paper provides specific guidelines for choosing the PVT model, black-oil or equation of state (EOS), for full-field reservoir simulation of volatile/near-critical oil and gas condensate fluid systems produced by depletion and/or gas injection. In the paper we have used a "generic" reservoir from the North Sea containing a fluid system with compositional grading from a medium-rich gas condensate upstructure, through an undersaturated critical mixture at the gas-oil contact, to a volatile oil downstructure. A component pseudoization procedure is described which involves a stepwise automated regression from the original 22-component EOS. We found that a six-component pseudoized EOS model described the reservoir fluid system with good accuracy and, for the most part, this EOS model was used in the study. Methods are proposed for generating consistent black-oil PVT tables for this complex fluid system. The methods are based on consistent initialization and accurate in-place surface gas and surface oil volumes when compared with initialization with an EOS model. We also discuss the trade-off between accurate initialization and accurate depletion performance (oil and gas recoveries). Each "reservoir" is simulated using black-oil and compositional models for various depletion and gas injection cases. The simulated performance for the two PVT models is compared for fluid systems ranging from a medium rich gas condensate to a critical fluid, to slightly volatile oils. The initial reservoir fluid composition is either constant with depth or exhibits a vertical compositional gradient. Scenarios both with saturated and undersaturated GOC are considered. The reservoir performance for the two PVT models is also compared for different permeability distributions. Reservoir simulation results show that the black-oil model can be used for all depletion cases if the black-oil PVT data are generated properly. In most gas injection cases, the black-oil model is not recommended — with only a few exceptions. We also show that black-oil simulations using solution oil/gas ratio equal to zero (rs=0) does not always define a conservative ("P10") sensitivity for gas injection processes. If gravity segregation is strong, the incremental loss of oil recovery due to "zero vaporization" is more than offset by exaggerated density differences caused by erroneous gas densities.
Solvent‐Free Photooxidation of Alkanes by Dioxygen with 2,3‐Dichloro‐5,6‐dicyano‐p‐benzoquinone via Photoinduced Electron Transfer (2016)

Photooxidation of alkanes by dioxygen occurred under visible light irradiation of 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) which acts as a super photooxidant. Solvent-free hydroxylation of cyclohexane and alkanes is initiated by electron transfer from alkanes to the singlet and triplet excited states of DDQ to afford the corresponding radical cations and DDQ(⋅-) , as revealed by femtosecond laser-induced transient absorption measurements. Alkane radical cations readily deprotonate to produce alkyl radicals, which react with dioxygen to afford alkylperoxyl radicals. Alkylperoxyl radicals abstract hydrogen atoms from alkanes to yield alkyl hydroperoxides, accompanied by regeneration of alkyl radicals to constitute the radical chain reactions, so called autoxidation. The radical chain is terminated in the bimolecular reactions of alkylperoxyl radicals to yield the corresponding alcohols and ketones. DDQ(⋅-) , produced by the photoinduced electron transfer from alkanes to the excited state of DDQ, disproportionates with protons to yield DDQH2 .
Flexible Strategy for the Synthesis of Pyrrolizidine Alkaloids (2008)

A general strategy for the production of pyrrolizidine alkaloids is described, starting from intermediate (+)-9. The key features are diastereoselective dihydroxylation, inversion at the ring junction by hydroboration of an enamine, and ring closure to form the bicyclo ring system. This route is attractive because of its brevity and versatility; four natural products were prepared with differing stereochemistry and substitution patterns. Finally, this work allowed assignment of the absolute stereochemistry of 2,3,7-triepiaustraline and hyacinthacine A 7.
Testing for Gene-Gene Interaction with AMMI Models (2010)

Studies have shown that many common diseases are influenced by multiple genes and their interactions. There is currently a strong interest in testing for association between combinations of these genes and disease, in particular because genes that affect the risk of disease only in the presence of another genetic variant may not be detected in marginal analysis. In this paper we propose the use of additive main effect and multiplicative interaction (AMMI) models to detect and to quantify gene-gene interaction effects for a quantitative trait. The objective of the present research is to demonstrate the practical advantages of these models to describe complex interaction between two unlinked loci. Although gene-gene interactions have often been defined as a deviance from additive genetic effects, the residual term has generally not been appropriately treated. The AMMI models allow for the analysis of a two way factorial data structure and combine the analysis of variance of the two main genotype effects with a principal component analysis of the residual multiplicative interaction. The AMMI models for gene-gene interaction presented here allow for the testing of non additivity between the two loci, and also describe how their interaction structure fits the existing non-additivity. Moreover, these models can be used to identify the specific two genotypes combinations that contribute to the significant gene-gene interaction. We describe the use of the biplot to display the structure of the interaction and evaluate the performance of the AMMI and the special cases of the AMMI previously described by Tukey and Mandel with simulated data sets. Our simulated study showed that the AMMI model is as powerful as general linear models when the interaction is not modeled in the presence of marginal effects. However, in the presence of pure epitasis, i.e. in the absence of marginal effects, the AMMI method was not found to be superior to other tested regression methods.
Multiparametric ultrasound in the detection of prostate cancer: a systematic review (2015)

Available evidence confirms that combining different ultrasound modalities significantly improves diagnostic performance.
Towards Adaptive Quality Assurance in Industrial Applications (2022)

We propose the AQUILA framework (Adaptive Quality Assurance in Industrial Applications), a concept for digitalization in Industry 4.0 to support the entire industrial manufacturing chain, laying the groundwork for adaptive quality assurance in times of disrupted supply chains and, due to the COVID-19 pandemic, restricted travel possibilities. To that end, our proposed framework allows for the definition and description of industrial processes, quality assurance and testing protocols, and training scenarios in a comprehensive notation based on BPMN, and supports users in task execution, documentation, and evaluation by providing smart glass-based HCI with eye tracking technology, delivering a combination of process documentation, context-sensitive AR visualization, gaze-based interaction schemes, and remote maintenance and assistance functionality.
Blockade of Myeloid-Derived Suppressor Cell Expansion with All- Trans Retinoic Acid Increases the Efficacy of Antiangiogenic Therapy (2018)

Intrinsic and adaptive resistance hampers the success of antiangiogenic therapies (AAT), especially in breast cancer where this treatment modality has proven largely ineffective. Therefore, novel strategies to improve the efficacy of AAT are warranted. Solid tumors such as breast cancer are characterized by a high infiltration of myeloid-derived suppressor cells (MDSC), which are key drivers of resistance to AAT. Therefore, we hypothesized that all-<i>trans</i> retinoic acid (ATRA), which induces differentiation of MDSC into mature cells, could improve the therapeutic effect of AAT. ATRA increased the efficacy of anti-VEGFR2 antibodies alone and in combination with chemotherapy in preclinical breast cancer models. ATRA reverted the anti-VEGFR2-induced accumulation of intratumoral MDSC, alleviated hypoxia, and counteracted the disorganization of tumor microvessels. Mechanistic studies indicate that ATRA treatment blocked the AAT-induced expansion of MDSC secreting high levels of vessel-destabilizing S100A8. Thus, concomitant treatment with ATRA holds the potential to improve AAT in breast cancer and possibly other tumor types.<b>Significance:</b> Increasing the therapeutic efficiency of antiangiogenic drugs by reducing resistance-conferring myeloid-derived suppressor cells might improve breast cancer treatment.<b>Graphical Abstract:</b> http://cancerres.aacrjournals.org/content/canres/78/12/3220/F1.large.jpg <i>Cancer Res; 78(12); 3220-32. ©2018 AACR</i>.
New developments in magnetic resonance imaging techniques for shoulder instability in athletes (2010)

Magnetic resonance (MR) imaging can be a very useful tool in the evaluation of instability in the athlete's shoulder. Technical options of MR imaging, such as arthrography, higher power magnets, and shoulder positioning, have enhanced MR evaluation of the shoulder. This update discusses the application of new MR techniques to a variety of shoulder instability patterns, including anterior instability, posterior instability, and atraumatic multidirectional instability. Specific applications of MR imaging in the postoperative patient is discussed. Finally, we describe the future directions of MR imaging in the setting of shoulder instability.
Cationic cell-penetrating peptides interfere with TNF signalling by induction of TNF receptor internalization (2005)

Cationic cell-penetrating peptides (CPPs) have been used widely as delivery vectors for the import of molecules that otherwise do not cross the plasma membrane of eukaryotic cells. In this work, we demonstrate that the three cationic CPPs, Antennapedia homeodomain-derived peptide (Antp), nona-arginine and Tat-derived peptide, inhibit tumour necrosis factor (TNF)-mediated signal transduction. This inhibition is based on the downregulation of TNF receptors at the cell surface by induction of internalization. In contrast to TNF-dependent receptor internalization, no receptor activation occurs. The receptor downregulation is not restricted to the CPPs. Remarkably, the HIV-1 Tat protein itself also induces the internalization of TNF receptors. The dynamin dependence of the internalization, as well as the fact that epidermal growth factor receptors are also internalized, suggest a general induction of clathrin-dependent endocytosis as the mechanism of action. The significance of these findings for the use of cationic CPPs in the import of bioactive peptides is demonstrated here using a conjugate consisting of Antp and a Smac protein-derived cargo peptide. The cargo alone, when introduced into cells by electroporation, enhanced TNF-induced apoptosis by inhibiting the anti-apoptotic action of IAPs (inhibitor of apoptosis proteins). For the Antp-Smac conjugate at concentrations below 40 muM the inhibitory effect of the Antp peptide compensated for the pro-apoptotic activity of the cargo, and led to the protection of cells against TNF-mediated apoptosis. These data provide important new information for the use of cationic CPPs for the cellular delivery of bioactive molecules.
Minimally Invasive versus Open Posterior Lumbar Interbody Fusion: A Systematic Review (2014)

Based on the available evidence, which we restricted to prospective and retrospective studies with control groups, but did not include any well-designed randomized trials, MIS PLIF might lead to better perioperative parameters, but there was little evidence for improved patient-reported outcomes in the MIS groups. Randomized controlled trials are needed to compare these two surgical techniques.
Graded bit patterned magnetic arrays fabricated via angled low-energy He ion irradiation (2012)

A bit patterned magnetic array based on Co/Pd magnetic multilayers with a binary perpendicular magnetic anisotropy distribution was fabricated. The binary anisotropy distribution was attained through angled helium ion irradiation of a bit edge using hydrogen silsesquioxane (HSQ) resist as an ion stopping layer to protect the rest of the bit. The viability of this technique was explored numerically and evaluated through magnetic measurements of the prepared bit patterned magnetic array. The resulting graded bit patterned magnetic array showed a 35% reduction in coercivity and a 9% narrowing of the standard deviation of the switching field.