gebhart/patrepeval huggingface dataset:
A Coupled Multiscale Approach to Modeling Aortic Valve Mechanics in Health and Disease (2021)

Mechano-biological processes in the aortic valve span multiple length scales ranging from the molecular and cell to tissue and organ levels. The valvular interstitial cells residing within the valve cusps sense and actively respond to leaflet tissue deformations caused by the valve opening and closing during the cardiac cycle. Abnormalities in these biomechanical processes are believed to impact the matrix-maintenance function of the valvular interstitial cells, thereby initiating valvular disease processes such as calcific aortic stenosis. Understanding the mechanical behavior of valvular interstitial cells in maintaining tissue homeostasis in response to leaflet tissue deformation is therefore key to understanding the function of the aortic valve in health and disease. In this study, we applied a multiscale computational homogenization technique (also known as “FE2”) to aortic valve leaflet tissue to study the three-dimensional mechanical behavior of the valvular interstitial cells in response to organ-scale mechanical loading. We further considered calcific aortic stenosis with the aim of understanding the likely relationship between the valvular interstitial cell deformations and calcification. We find that the presence of calcified nodules leads to an increased strain profile that drives further growth of calcification.
Ruthenium(ii) catalysed synthesis of unsaturated oxazolines via arene C–H bond alkenylation (2012)

Monoalkenylation of arene C–H bonds directed by an oxazoline group to afford bifunctional alkenes is described using [RuCl2(p-cymene)]2 as the catalyst in the presence of 1,1′-binaphthyl-2,2′-diyl hydrogenphosphate (BNPAH) and of Cu(OAc)2·H2O under air. This reaction takes place under mild conditions in ethanol at 80 °C and tolerates the oxazoline function.
Alizarin Complexone on Nanocrystalline TiO<sub>2</sub>: A Heterogeneous Approach to Anion Sensing (2004)

Abstract A novel, heterogeneous approach to “naked‐eye” colorimetric and spectrophotometric anion sensing is demonstrated, employing the molecular receptor alizarin complexone adsorbed onto a nanocrystalline, mesoporous TiO 2 film. pH buffer action intrinsic to the TiO 2 film allows dip sensing in aqueous solutions. This heterogeneous sensing system exhibits a high selectivity to F – and CN – anions, high sensitivity, a rapid response time, and excellent reusability.
Surface Electronic Structures and Photoluminescence Mechanisms of Porous Si (1996)

Surface structures and photoluminescence (PL) mechanisms of porous Si (PS) and the role of oxygen termination on PS have been investigated using a synchrotron‐radiation photoemission spectroscopy technique, an Auger electron spectroscopy technique, and a photoluminescence technique. There is almost no trace of oxygen on the surface of as‐anodized PS and its surface is covered with hydrides. An increase in PL intensity with increasing anodization current is interpreted to correspond to an increase in the number of photoluminescent elements. The investigation on the oxidation effect suggests that oxygen termination itself does not affect electronic transition levels unless it modifies the size or the structure of the Si crystallites. Energy bandgap analysis indicates that PL peak energy of PS correlates well to the surface energy gap, and that values of energy gaps and exciton energies obtained for PS are close to the results of the recent theoretical calculations for quantum dots and wires.
Discovery of 7-[<sup>18</sup>F]Fluorotryptophan as a Novel Positron Emission Tomography (PET) Probe for the Visualization of Tryptophan Metabolism in Vivo (2017)

Tryptophan and its metabolites are involved in different physiological and pathophysiological processes. Consequently, positron emission tomography (PET) tracers addressing tryptophan metabolic pathways should allow the detection of different pathologies like neurological disorders and cancer. Herein we report an efficient method for the preparation of fluorotryptophans labeled in different positions with <sup>18</sup>F and their biological evaluation. 4-7-[<sup>18</sup>F]Fluorotryptophans ([<sup>18</sup>F]FTrps) were prepared according to a modified protocol of alcohol-enhanced Cu-mediated radiofluorination in 30-53% radiochemical yields. In vitro experiments demonstrated high cellular uptake of 4-7-[<sup>18</sup>F]FTrps in different tumor cell lines. 4, 5-, and 6-[<sup>18</sup>F]FTrps, although stable in vitro, suffered from rapid in vivo defluorination. In contrast, 7-[<sup>18</sup>F]FTrp demonstrated a high in vivo stability and enabled a clear delineation of serotonergic areas and melatonin-producing pineal gland in rat brains. Moreover 7-[<sup>18</sup>F]FTrp accumulated in different tumor xenografts in a chick embryo CAM model. Thus, 7-[<sup>18</sup>F]FTrp represents a highly promising PET probe for imaging of Trp metabolism.
A Qualitative Investigation of Deposition Velocities of a Non-Newtonian Slurry in Complex Pipeline Geometries (2009)

The External Flowsheet Review Team (EFRT) has identified the issues relating to the Waste Treatment and Immobilization Plant (WTP) pipe plugging. Per the review’s executive summary, “Piping that transports slurries will plug unless it is properly designed to minimize this risk. This design approach has not been followed consistently, which will lead to frequent shutdowns due to line plugging.” To evaluate the potential for plugging, testing was performed to determine critical velocities for the complex WTP piping layout. Critical velocity is defined as the point at which a moving bed of particles begins to form on the pipe bottom during slurry-transport operations. Pressure drops across the fittings of the test pipeline were measured with differential pressure transducers, from which the critical velocities were determined. A WTP prototype flush system was installed and tested upon the completion of the pressure-drop measurements. We also provide the data for the overflow relief system represented by a WTP complex piping geometry with a non-Newtonian slurry. A waste simulant composed of alumina (nominally 50 μm in diameter) suspended in a kaolin clay slurry was used for this testing. The target composition of the simulant was 10 vol% alumina in a suspending medium with a yield stress of 3 Pa. No publications or reports are available to confirm the critical velocities for the complex geometry evaluated in this testing; therefore, for this assessment, the results were compared to those reported by Poloski et al. (2008) for which testing was performed for a straight horizontal pipe. The results of the flush test are compared to the WTP design guide 24590-WTP-GPG-M-0058, Rev. 0 (Hall 2006) in an effort to confirm flushing-velocity requirements.
Purkinje‐Related Arrhythmias Part I: Monomorphic Ventricular Tachycardias (2011)

Purkinje-related monomorphic ventricular tachycardias (VTs) can be classified into four distinct groups: (1) verapamil-sensitive left fascicular VT, (2) Purkinje fiber-mediated VT post infarction, (3) bundle branch reentry (BBR) and interfascicular reentry VTs, and (4) focal Purkinje VT. There are three subtypes of fascicular VTs: (1) left posterior fascicular VT with a right bundle branch block (RBBB) configuration and superior axis; (2) left anterior fascicular VT with an RBBB configuration and right-axis deviation; and (3) upper septal fascicular VT with a narrow QRS configuration. The mechanism of the fascicular VT is macroreentry. While the antegrade limb of the circuit is a midseptal abnormal Purkinje fiber in the anterior and posterior fascicular VTs, the antegrade limb of the upper septal fascicular VT is both the anterior and posterior fascicles, and the retrograde limb is a midseptal abnormal Purkinje fiber. Purkinje fiber-mediated VT post infarction also exhibits verapamil sensitivity, and the surviving muscle bundles within the myocardium and Purkinje system are components of the reentry circuit. BBR-VT and interfascicular reentry VT are amenable to being cured by the creation of bundle or fascicular block. The mechanism of focal Purkinje VT is abnormal automaticity from the distal Purkinje system, and the ablation target is the earliest Purkinje activation during the VT. It is difficult to distinguish verapamil-sensitive fascicular VT from focal Purkinje VT by the 12-lead electrocardiogram; however, focal Purkinje VT is not responsive to verapamil . The recognition of the heterogeneity of these VTs and their unique characteristics should facilitate an appropriate diagnosis and therapy.
Cytokine Release Syndrome Associated with T-Cell-Based Therapies for Hematological Malignancies: Pathophysiology, Clinical Presentation, and Treatment (2021)

Cytokines are a broad group of small regulatory proteins with many biological functions involved in regulating the hematopoietic and immune systems. However, in pathological conditions, hyperactivation of the cytokine network constitutes the fundamental event in cytokine release syndrome (CRS). During the last few decades, the development of therapeutic monoclonal antibodies and T-cell therapies has rapidly evolved, and CRS can be a serious adverse event related to these treatments. CRS is a set of toxic adverse events that can be observed during infection or following the administration of antibodies for therapeutic purposes and, more recently, during T-cell-engaging therapies. CRS is triggered by on-target effects induced by binding of chimeric antigen receptor (CAR) T cells or bispecific antibody to its antigen and by subsequent activation of bystander immune and non-immune cells. CRS is associated with high circulating concentrations of several pro-inflammatory cytokines, including interleukins, interferons, tumor necrosis factors, colony-stimulating factors, and transforming growth factors. Recently, considerable developments have been achieved with regard to preventing and controlling CRS, but it remains an unmet clinical need. This review comprehensively summarizes the pathophysiology, clinical presentation, and treatment of CRS caused by T-cell-engaging therapies utilized in the treatment of hematological malignancies.
Microfluidic deposition for resolving single-molecule protein architecture and heterogeneity (2018)

Scanning probe microscopy provides a unique window into the morphology, mechanics, and structure of proteins and their complexes on the nanoscale. Such measurements require, however, deposition of samples onto substrates. This process can affect conformations and assembly states of the molecular species under investigation and can bias the molecular populations observed in heterogeneous samples through differential adsorption. Here, we show that these limitations can be overcome with a single-step microfluidic spray deposition platform. This method transfers biological solutions to substrates as microdroplets with subpicoliter volume, drying in milliseconds, a timescale that is shorter than typical diffusion times of proteins on liquid-solid interfaces, thus avoiding surface mass transport and change to the assembly state. Finally, the single-step deposition ensures the attachment of the full molecular content of the sample to the substrate, allowing quantitative measurements of different molecular populations within heterogeneous systems, including protein aggregates.
Isomer-Resolved Imaging of Prostate Cancer Tissues Reveals Specific Lipid Unsaturation Profiles Associated With Lymphocytes and Abnormal Prostate Epithelia (2021)

Prostate cancer is the fourth most common cancer worldwide with definitive diagnosis reliant on biopsy and human-graded histopathology. As with other pathologies, grading based on classical haematoxylin and eosin (H&E) staining of formalin fixed paraffin-embedded material can be prone to variation between pathologists, prompting investigation of biomolecular markers. Comprising around 50% of cellular mass, and with known metabolic variations in cancer, lipids provide a promising target for molecular pathology. Here we apply isomer-resolved lipidomics in combination with imaging mass spectrometry to interrogate tissue sections from radical prostatectomy specimens. Guided by the histopathological assessment of adjacent tissue sections, regions of interest are investigated for molecular signatures associated with lipid metabolism, especially desaturation and elongation pathways. Monitoring one of the most abundant cellular membrane lipids within these tissues, phosphatidylcholine (PC) 34:1, high positive correlation was observed between the n-9 isomer (site of unsaturation 9-carbons from the methyl terminus) and epithelial cells from potential pre-malignant lesions, while the n-7 isomer abundance was observed to correlate with immune cell infiltration and inflammation. The correlation of lipid isomer signatures with human disease states in tissue suggests a future role for isomer-resolved mass spectrometry imaging in assisting pathologists with prostate cancer diagnoses and patient stratification.
A Review on PARP1 Inhibitors: Pharmacophore Modeling, Virtual and Biological Screening Studies to Identify Novel PARP1 Inhibitors (2014)

A tremendous research on Poly (ADP-ribose) polymerase (PARP) pertaining to cancer and ischemia is in very rapid progress. PARP's are a specific class of enzymes that repairs the damaged DNA. Recent findings suggest also that PARP-1 is the most abundantly expressed nuclear enzyme which involves in various therapeutic areas like inflammation, stroke, cardiac ischemia, cancer and diabetes. The current review describes the overview on clinical candidates of PARP1 and its current status in clinical trials. This paper also covers identification of potent PARP1 inhibitors using structure and ligand based pharmacophore models. Finally 36 potential hits were identified from the virtual screening of pharmacophore models and screened for PARP1 activity. 15 actives were identified as potent PARP1 inhibitors and further optimization of these analogues are in progress.
Association of Polymorphisms in Neuroprotection and Oxidative Stress Genes and Neurodevelopmental Outcomes After Preterm Birth (2020)

To estimate the associations between neuronal homeostasis, neuroprotection, and oxidative stress candidate gene polymorphisms and neurodevelopmental disability.
Interleukin-1  Producing Synovial Sarcoma with Prolonged Fever: a Case Report (1998)

The patient had a synovial sarcoma of the monophasic fibrous type accompanied by prolonged spike fever. Wide excision of the tumor resulted in the disappearance of her fever. The tumor cells showed interleukin-1 alpha (IL-1 alpha) expression immunohistochemically. IL-1 alpha cDNA was detected in the tumor by RT-PCR, the sequences of which were identical with those of normal human IL-1 alpha molecules. These results indicated that IL-1 alpha, one of the fever-inducing cytokines, was expressed by sarcoma cells in the present case, which were thought to be a causative factor of the fever.
Race-Related Differences in the Clinical Presentation and Histopathologic Features of Phyllodes Tumor (2021)

In this single-institution retrospective study, we observed disproportionate rates of aggressive histopathologic features and disparate outcomes among black women with PT. A multi-institutional PT registry would facilitate improved knowledge about race-related differences in the presentation and outcomes of this rare tumor.
Anterior and Posterior Lamellar Graft on the Same Eye to Treat Fuchs Endothelial Corneal Dystrophy: the “Corneal Sandwich Graft” (2017)

Currently, the standard care for patients with endothelial dysfunction is a posterior lamellar graft which can be performed either as Descemetʼs stripping automated endothelial keratoplasty (DSAEK) or Descemetʼs membrane endothelial keratoplasty (DMEK). Posterior lamellar keratoplasty (PLK) is nowadays preferred over penetrating keratoplasty (PK) because of quicker visual recovery, less astigmatism and lower rate of rejection [1]. However, longstanding stromal edema in patients with endothelial dysfunction can lead to temporary or even persistent subepithelial haze or scarring [2]. Espana et al. studied confocal microscopic features in patients with Fuchs endothelial dystrophy (FED) and pseudophakic bullous keratopathy who underwent DSAEK and correlated these findings with the post operative visual acuity. They concluded that the most important limiting factor for improvement of best-corrected visual acuity (BCVA) was subepithelial haze [2]. These opacities can cause irregular anterior corneal surface and visual distortions, which may persist even after DSAEK [3]. To date, the only way to treat this was to perform a PK.
Immune Receptors Involved in Streptococcus suis Recognition by Dendritic Cells (2012)

Streptococcus suis is an important swine pathogen and an emerging zoonotic agent of septicemia and meningitis. Knowledge on host immune responses towards S. suis, and strategies used by this pathogen for subversion of these responses is scarce. The objective of this study was to identify the immune receptors involved in S. suis recognition by dendritic cells (DCs). Production of cytokines and expression of co-stimulatory molecules by DCs were shown to strongly rely on MyD88-dependent signaling pathways, suggesting that DCs recognize S. suis and become activated mostly through Toll-like receptor (TLR) signaling. Supporting this fact, TLR2(-/-) DCs were severely impaired in the release of several cytokines and the surface expression of CD86 and MHC-II. The release of IL-12p70 and CXC10, and the expression of CD40 were found to depend on signaling by both TLR2 and TLR9. The release of IL-23 and CXCL1 were partially dependent on NOD2. Finally, despite the fact that MyD88 signaling was crucial for DC activation and maturation, MyD88-dependent pathways were not implicated in S. suis internalization by DCs. This first study on receptors involved in DC activation by S. suis suggests a major involvement of MyD88 signaling pathways, mainly (but not exclusively) through TLR2. A multimodal recognition involving a combination of different receptors seems essential for DC effective response to S. suis.
Functional Characterization of Gne (UDP- <i>N</i> -Acetylglucosamine- 4-Epimerase), Wzz (Chain Length Determinant), and Wzy (O-Antigen Polymerase) of <i>Yersinia enterocolitica</i> Serotype O:8 (2002)

The lipopolysaccharide (LPS) O-antigen of Yersinia enterocolitica serotype O:8 is formed by branched pentasaccharide repeat units that contain N-acetylgalactosamine (GalNAc), L-fucose (Fuc), D-galactose (Gal), D-mannose (Man), and 6-deoxy-D-gulose (6d-Gul). Its biosynthesis requires at least enzymes for the synthesis of each nucleoside diphosphate-activated sugar precursor; five glycosyltransferases, one for each sugar residue; a flippase (Wzx); and an O-antigen polymerase (Wzy). As this LPS shows a characteristic preferred O-antigen chain length, the presence of a chain length determinant protein (Wzz) is also expected. By targeted mutagenesis, we identify within the O-antigen gene cluster the genes encoding Wzy and Wzz. We also present genetic and biochemical evidence showing that the gene previously called galE encodes a UDP-N-acetylglucosamine-4-epimerase (EC 5.1.3.7) required for the biosynthesis of the first sugar of the O-unit. Accordingly, the gene was renamed gne. Gne also has some UDP-glucose-4-epimerase (EC 5.1.3.2) activity, as it restores the core production of an Escherichia coli K-12 galE mutant. The three-dimensional structure of Gne was modeled based on the crystal structure of E. coli GalE. Detailed structural comparison of the active sites of Gne and GalE revealed that additional space is required to accommodate the N-acetyl group in Gne and that this space is occupied by two Tyr residues in GalE whereas the corresponding residues present in Gne are Leu136 and Cys297. The Gne Leu136Tyr and Cys297Tyr variants completely lost the UDP-N-acetylglucosamine-4-epimerase activity while retaining the ability to complement the LPS phenotype of the E. coli galE mutant. Finally, we report that Yersinia Wzx has relaxed specificity for the translocated oligosaccharide, contrary to Wzy, which is strictly specific for the O-unit to be polymerized.
Smart Data Analytics in SME Manufacturing – an Axiomatic Design based Conceptual Framework (2019)

The objective of this paper is to go a step further introducing the concept of Industry 4.0 (I4.0) using Axiomatic Design as a research methodology. The rationale for this work is to increase the performance of SMEs allowing a better utilization of resources, using tools coming to the foreground of industry enabled by the Fourth Industrial Revolution (also known as Industry 4.0). This would improve the competitive position of SMEs on the global market. The state-of-the-art shows that only few companies andespecially few small and medium sized enterprises (SMEs) are using data analytics to take advantage of new technological achievements to compete with one another. The method used in this paper for deriving aconceptual framework how SMEs can exploit the advantages of smart data analytics in manufacturing is axiomatic design, using inputs collected from a field study at SMEs. The results show that SMEs are challenged in implementing advanced data analytics instruments and need to define strategies for collecting, analysing and interpreting data for improving their performance and provide framework which should help SMEs to implement data analytics on the shop floor.
Management of acute promyelocytic leukemia: recommendations from an expert panel on behalf of the European LeukemiaNet (2008)

The introduction of all-trans retinoic acid (ATRA) and, more recently, arsenic trioxide (ATO) into the therapy of acute promyelocytic leukemia (APL) has revolutionized the management and outcome of this disease. Several treatment strategies using these agents, usually in combination with chemotherapy, but also without or with minimal use of cytotoxic agents, have provided excellent therapeutic results. Cure of APL patients, however, is also dependent on peculiar aspects related to the management and supportive measures that are crucial to counteract life-threatening complications associated with the disease biology and molecularly targeted treatment. The European LeukemiaNet recently appointed an international panel of experts to develop evidence- and expert opinion-based guidelines on the diagnosis and management of APL. Together with providing current indications on genetic diagnosis, modern risk-adapted front-line therapy and salvage treatment, the review contains specific recommendations for the identification and management of most important complications such as the bleeding disorder, APL differentiation syndrome, QT prolongation and other ATRA- and ATO-related toxicities, as well as for molecular assessment of response to treatment. Finally, the approach to special situations is also discussed, including management of APL in children, elderly patients, and pregnant women.
Multiresonant High-<i>Q</i> Plasmonic Metasurfaces (2019)

Resonant metasurfaces are devices composed of nanostructured subwavelength scatterers that generate narrow optical resonances, enabling applications in filtering, nonlinear optics, and molecular fingerprinting. It is highly desirable for these applications to incorporate such devices with multiple high-quality-factor resonances; however, it can be challenging to obtain more than a pair of narrow resonances in a single plasmonic surface. Here, we demonstrate a multiresonant metasurface that operates by extending the functionality of surface lattice resonances, which are the collective responses of arrays of metallic nanoparticles. This device features a series of resonances with high-quality factors (<i>Q</i> ∼ 40), an order of magnitude larger than what is typically achievable with plasmonic nanoparticles, as well as a narrow free spectral range. This design methodology can be used to better tailor the transmission spectrum of resonant metasurfaces and represents an important step toward the miniaturization of optical devices.