gebhart/patrepeval huggingface dataset:
Thermal and Geomechanical Dynamics of High Power Electromagnetic Heating of Rocks (2017)

Abstract Perforation is an essential step in the cased completion of oil and gas wells, since it provides channels for hydrocarbon fluids to flow from the reservoir into production wells. Traditional methods for perforation cause plastic compaction, resulting in permeability loss in the rock around the perforation channels and reduction of the hydraulic conductivity in the surrounding rock formation. A feasible alternative is to use high power electromagnetic (HPEM) sources to induce a localized phase change in the rock via dielectric heating and create a perforation. This method has crucial benefits: it is contactless, waterless, improves conductivity, and reduces general damage to the rock formation. The physical dynamics that makes this possible have been extensively documented in several experimental studies, and some numerical models have been proposed to simulate the thermal mechanical coupling between the HPEM source and the rock for perforation and other stimulation operations. Yet, due to the inherent multi-scale complexity of the physics involved, a comprehensive model remains a topic of advanced research. Recently, a numerical scheme was proposed to predict the perforation geometry and production enhancements as a function of the HPEM source parameters (beam shape and energy distribution), rock properties, and stress configuration. This paper expands this workflow to investigate the effects of material heterogeneity and stress configuration on the perforation rate and the rock's morphology resulting from HPEM heating. The numerical model is based on a hybrid COMSOL-FLAC coupling. In a companion paper, this model is extended to describe the effect of long-pulsed thermal incidence and rock morphology using the thermal and continuum mechanic modules in FLAC.
Cannabinoid CB2 receptor ligand profiling reveals biased signalling and off-target activity (2017)

The cannabinoid CB<sub>2</sub> receptor (CB<sub>2</sub>R) represents a promising therapeutic target for various forms of tissue injury and inflammatory diseases. Although numerous compounds have been developed and widely used to target CB<sub>2</sub>R, their selectivity, molecular mode of action and pharmacokinetic properties have been poorly characterized. Here we report the most extensive characterization of the molecular pharmacology of the most widely used CB<sub>2</sub>R ligands to date. In a collaborative effort between multiple academic and industry laboratories, we identify marked differences in the ability of certain agonists to activate distinct signalling pathways and to cause off-target effects. We reach a consensus that HU910, HU308 and JWH133 are the recommended selective CB<sub>2</sub>R agonists to study the role of CB<sub>2</sub>R in biological and disease processes. We believe that our unique approach would be highly suitable for the characterization of other therapeutic targets in drug discovery research.
Comprehensive Analysis of the Prognostic Significance of the TRIM Family in the Context of TP53 Mutations in Cancers (2023)

The p53 protein is an important tumor suppressor, and TP53 mutations are frequently associated with poor prognosis in various cancers. Mutations in TP53 result in a loss of p53 function and enhanced expression of cell cycle genes, contributing to the development and progression of cancer. Meanwhile, several tripartite motif (TRIM) proteins are known to regulate cell growth and cell cycle transition. However, the prognostic values between TP53 and TRIM family genes in cancer are unknown. In this study, we analyzed the relationship between the <i>TP53</i> mutations and TRIM family proteins and evaluated the prognostic significance of TRIM family proteins in cancer patients with P53 mutations. Our findings identified specific TRIM family members that are upregulated in <i>TP53</i> mutant tumors and are associated with the activation of genes related to a cell-cycle progression in the context of TP53 mutations.
Dynamic flow quantitation with spatial orientation guided digital color Doppler imaging: <i>In vitro</i> validation and initial <i>in vivo</i> experience (1998)

The assumptions of geometric shape and uniform velocity profile prohibit the use of conventional Doppler methods for volume flow quantification with irregularly shaped nonvascular passages in space. A flow quantification method that integrates a three-dimensional (3-D) position and orientation sensing system with digital color Doppler imaging approach has been developed. Methods: The optimized ultrasound system settings were predetermined using a static, laminar flow model. The instantaneous flow rate was measured by the integration of the area-velocity product with angle correction. Initial in vivo studies quantified gastric emptying on five healthy volunteers 10 min after ingestion of a 500-ml meat soup, postprandially. Digital Doppler images were obtained continuously covering a transpyloric flow episode, immediately following the 3-D scan of the passage. The flow direction was derived from 3-D reconstruction using the centroids of two short-axis views. Results: In vitro validation showed the Doppler flow rates were within 10% for reference flow rates ranging from 6 to 30 ml/s. The average gastric emptying lasted 0.75 s with 3.0 ml in volume. Conclusions: With appropriate instrument settings, orientation determined digital Doppler can be used for the quantification of gastric emptying with adequate accuracy. This method minimized the angular ambiguity and geometric assumptions.
10.1016/s0967-0653(98)83801-5 (2000)

Abstract Coastal cities are critical areas for global environmental change, but they have not been a focus of study in coastal zone management or urban planning. This paper lays the conceptual groundwork for such a focus, based on an ‘ecomanagement’ or ecosystem approach. The unique ‘bi-polar’ aspect of the juxtaposition of a complex natural system with a complex built system is stressed and explored. Among the benefits of an ecosystem approach is that it provides a common, scientifically defensible, ground for diverse visions and jurisdictions in a designated area. The history of recent ecosystemic and metabolic studies of cities is reviewed, as well as the implications of the intensification of use of the natural ecosystem for coastal city purposes. A series of brief case studies of developed and developing country cities is presented: Dakar, Hanoi, Alexandria, Toronto, and Venice. Finally, some of the implications of studying coastal cities in the context of rapid global change are outlined, as a preliminary agenda for further research.
Novel Inhibitors of Fatty Acid Oxidation as Potential Metabolic Modulators. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Surgical strategy for an adult patient with a catecholamine-producing ganglioneuroblastoma and a cerebral aneurysm: a case report (2018)

Careful perioperative management is needed for a patient with both a catecholamine-producing tumor and cerebral aneurysm.
CCSP deficiency does not alter surfactant homeostasis during adenoviral infection (1999)

Clara cell secretory protein (CCSP) deficiency in mice is associated with increased susceptibility to pulmonary inflammation after hyperoxia or viral infection. Because adenoviral exposure perturbs pulmonary surfactant homeostasis in vivo, we hypothesized that CCSP deficiency would influence surfactant metabolism after pulmonary infection. Alveolar and total lung saturated phosphatidylcholine pool sizes were similar in CCSP-deficient [CCSP(-/-)] and wild-type [CCSP(+/+)] mice before and 7 days after intratracheal administration of adenovirus. Radiolabeled choline and palmitate incorporation into saturated phosphatidylcholine was similar, and there was no alteration by previous infection 7 days before the incorporation measurements. Furthermore, CCSP deficiency did not influence clearance of [(14)C]dipalmitoylphosphatidylcholine and (125)I-labeled recombinant surfactant protein C. Increased persistence of alveolar capillary leak was observed in CCSP(-/-) mice after adenoviral infection. Surfactant lipid homeostasis was not influenced by CCSP before or after administration of adenovirus to the lung. Persistence of alveolar capillary leak in CCSP(-/-) mice after adenovirus provides further evidence for the role of CCSP in the regulation of pulmonary inflammation.
Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth (2016)

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.
Performance of the auxiliary resonant commutated pole converter in converter based utility devices (2002)

In this paper the performance of the auxiliary resonant commutated pole converter is investigated experimentally for converter based utility devices. Converter performance is evaluated at high power and the results are compared with hard switched converter technology.
The Value and Relevance of T‐cell Lymphoma Registries (2021)

Peripheral T-cell lymphomas (PTCLs) comprise a heterogeneous group of neoplasms that are derived from post-thymic lymphoid cells at different stages of differentiation with diverse morphological patterns, phenotypes, and clinical presentation. To overcome the intrinsic limitations of population-based cancer registries and retrospective studies, the International Peripheral T-Cell and Natural Killer/T-Cell Lymphoma Study launched the T Cell Project, to verify whether a prospective collection of data would allow achieving more accurate information on T-cell lymphomas. The COMPLETE database was used for analyzing the diagnostic work-up of PTCLs in US clinical practice. One more contribution coming from the COMPLETE registry was the analysis on the role of autologous stem-cell transplantation in patients with newly diagnosed PTCL and in first complete remission. The search for ctDNA in PTCL may be a useful analysis to assess disease response and to predict relapse.
Leukotorien B4 receptor type 2 (BLT2) accelerates the healing of intestinal injury via promoting cell proliferation (2019)

BLT2, a low-affinity leukotriene B4 (LTB4) receptor, is highly expressed in intestinal epithelial cells. Recently, 12(S)-hydroxyheptadeca-5Z,8E,10E-trienoic acid (12-HHT) was identified as an endogenous ligand for BLT2. However, the precise role of this receptor has not been fully understood. The present study investigated the role of BLT2 in the healing of intestinal injury using BLT2-deficient (BLT2KO) mice, transgenic mice with intestinal epithelium-specific overexpression of BLT2 (villin-BLT2-Tg), and murine epithelial cell line (YAMC). The intestinal injury was induced in mice by subcutaneous administration of indomethacin and the healing of injury was determined 48, 72 and 96 h later. The wound (diameter: 1 mm) was inflicted on monolayer of YAMC and wound closure was evaluated 6 h later. Further, cell proliferation was determined by WST-1 assay. The healing of indomethacin-induced intestinal injury was significantly delayed in BLT2KO mice when compared with wild-type (WT) mice. In contrast, villin-BLT2-Tg mice exhibited healing-promoting properties when compared with WT mice. In YAMC, CAY10583, a BLT2 agonist, concentration-dependently promoted wound repair and cell proliferation. The similar effect was observed by 12-HHT. These findings suggest that BLT2 accelerates the healing of intestinal injury. This effect is at least partly mediated via promotion of epithelial cell proliferation.
Unraveling the Effect of PbI<sub>2</sub> Concentration on Charge Recombination Kinetics in Perovskite Solar Cells (2015)

CH3NH3PbI3 perovskite solar cells have rapidly risen to the forefront of emerging photovoltaic technologies. A solution-based, two-step method was reported to enhance the reproducibility of these solar cells. In this method, first a coating of PbI2 is applied by spin-coating onto a TiO2-coated substrate, followed by a dip in a methylammonium iodide solution, leading to conversion to CH3NH3PbI3. The concentration of PbI2 in the spin-coating solution is a very important factor that affects the infiltration of the perovskite and the amount deposited. The best solar cell performance of 13.9% was obtained by devices prepared using 1.0 M of PbI2 in dimethylformamide. These devices also had the longest electron lifetime and shortest carrier transport time, yielding lowest recombination losses. Rapid quenching of the perovskite emission is found in device-like structures, suggesting reasonably good efficient carrier extraction at the TiO2 interface and quantitative extraction at the spiro–OMeTAD interface.
Figure S1 from Baseline Tumor Size Is an Independent Prognostic Factor for Overall Survival in Patients with Melanoma Treated with Pembrolizumab (2023)

&lt;p&gt;Supplemental Figure&lt;/p&gt;
Novel control architecture for dual-output DC-DC converters driving DC-AC inversion system (2016)

To interface low-voltage dc-output power sources to ac grid, the split dc-bus dc-ac inverters driven by step-up isolated dual-output dc-dc converters can be a solution. When the split dc-bus dc-ac inverter is loaded with single-phase ac or unbalanced three-phase ac, current ripples will propagate through the dc-dc converters at frequencies that are related to the ac side fundamental. For the dc-dc converter close-loop voltage regulation to be robust against the disturbance introduced by those low frequency current ripples, a novel control architecture is proposed. In this paper, a combined control structure for dual-output dc-dc converters with common mode (CM) and differential mode (DM) compensation loops are presented. Simulation and experimental results have been provided for validation.
Dynamic Control of a Distributed Embedded Electro-Hydraulic System (2007)

&lt;div class="htmlview paragraph"&gt;This paper presents the hardware and software architectures, and the control approaches for a distributed embedded electro-hydraulic system, a telescopic handler. The distributed architecture is justified not only by the complexity of the vehicle architecture, consisting of mechanical, electrical and hydraulic components, but also by the existence of multiple types of communication protocols. The distributed architecture enables a hierarchical control strategy with the system-level control algorithms developed in Matlab/Simulink and implemented for the vehicle's two primary subsystems, work and propel-by-wire.&lt;/div&gt;
Heterogeneity in Human Induced Pluripotent Stem Cell–derived Alveolar Epithelial Type II Cells Revealed with ABCA3/SFTPC Reporters (2021)

Alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of lung alveoli, are typically identified through the use of the canonical markers, SFTPC and ABCA3. Self-renewing AEC2-like cells have been generated from human induced pluripotent stem cells (iPSCs) through the use of knock-in SFTPC fluorochrome reporters. However, developmentally, SFTPC expression onset begins in the fetal distal lung bud tip and thus is not specific to mature AEC2s. Furthermore, SFTPC reporters appear to identify only those iPSC-derived AEC2s (iAEC2s) expressing the highest SFTPC levels. Here, we generate an ABCA3 knock-in GFP fusion reporter (ABCA3:GFP) that enables the purification of iAEC2s while allowing visualization of lamellar bodies, organelles associated with AEC2 maturation. Using an SFTPC<sup>tdTomato</sup> and ABCA3:GFP bifluorescent line for <i>in vitro</i> distal lung-directed differentiation, we observe later onset of ABCA3:GFP expression and broader identification of the subsequently emerging iAEC2 population based on ABCA3:GFP expression compared with SFTPC<sup>tdTomato</sup> expression. Comparing ABCA3:GFP/SFTPC<sup>tdTomato</sup> double-positive with ABCA3:GFP single-positive (SP) cells by RNA sequencing and functional studies reveals iAEC2 cellular heterogeneity with both populations functionally processing surfactant proteins but the SP cells exhibiting faster growth kinetics, increased clonogenicity, increased expression of progenitor markers, lower levels of SFTPC expression, and lower levels of AEC2 maturation markers. Over time, we observe that each population (double-positive and SP) gives rise to the other and each can serve as the parents of indefinitely self-renewing iAEC2 progeny. Our results indicate that iAEC2s are a heterogeneous population of cells with differing proliferation versus maturation properties, the majority of which can be tracked and purified using the ABCA3:GFP reporter or surrogate cell surface proteins, such as SLC34A2 and CPM.
Compressive object tracking and classification using deep learning for infrared videos (2019)

Object tracking and classification in infrared videos are challenging due to large variations in illumination, target sizes, and target orientations. Moreover, if the infrared videos only generate compressive measurements, then it will be even more difficult to perform target tracking and classification directly in the compressive measurement domain, as many conventional trackers and classifiers can only handle reconstructed frames from compressive measurements. This paper summarizes our research effort on target tracking and classification directly in the compressive measurement domain. We focus on one special type of compressive measurement using pixel subsampling. That is, the original pixels in the video frames are randomly subsampled. Even in such special compressive sensing setting, conventional trackers do not work in a satisfactory manner. We propose a deep learning approach that integrates YOLO (You Only Look Once) and ResNet (residual network) for multiple target tracking and classification. YOLO is used for multiple target tracking and ResNet is for target classification. Extensive experiments using short wave infrared (SWIR) videos demonstrated the efficacy of the proposed approach even though the training data are very scarce.
Mechanisms of Cognitive Impairment in Cerebral Small Vessel Disease: Multimodal MRI Results from the St George's Cognition and Neuroimaging in Stroke (SCANS) Study (2013)

Cerebral small vessel disease (SVD) is a common cause of vascular cognitive impairment. A number of disease features can be assessed on MRI including lacunar infarcts, T2 lesion volume, brain atrophy, and cerebral microbleeds. In addition, diffusion tensor imaging (DTI) is sensitive to disruption of white matter ultrastructure, and recently it has been suggested that additional information on the pattern of damage may be obtained from axial diffusivity, a proposed marker of axonal damage, and radial diffusivity, an indicator of demyelination. We determined the contribution of these whole brain MRI markers to cognitive impairment in SVD. Consecutive patients with lacunar stroke and confluent leukoaraiosis were recruited into the ongoing SCANS study of cognitive impairment in SVD (n = 115), and underwent neuropsychological assessment and multimodal MRI. SVD subjects displayed poor performance on tests of executive function and processing speed. In the SVD group brain volume was lower, white matter hyperintensity volume higher and all diffusion characteristics differed significantly from control subjects (n = 50). On multi-predictor analysis independent predictors of executive function in SVD were lacunar infarct count and diffusivity of normal appearing white matter on DTI. Independent predictors of processing speed were lacunar infarct count and brain atrophy. Radial diffusivity was a stronger DTI predictor than axial diffusivity, suggesting ischaemic demyelination, seen neuropathologically in SVD, may be an important predictor of cognitive impairment in SVD. Our study provides information on the mechanism of cognitive impairment in SVD.
Ferroelectric Domain Wall Injection (2013)

Ferroelectric domain wall injection has been demonstrated by engineering of the local electric field, using focused ion beam milled defects in thin single crystal lamellae of KTiOPO4 (KTP). The electric field distribution (top) displays localized field hot-spots, which correlate with nucleation events (bottom). Designed local field variations can also dictate subsequent domain wall mobility, demonstrating a new paradigm in ferroelectric domain wall control.
Equilibrium Intermediates in the Denaturation of Human Insulin and Two Monomeric Insulin Analogs (1994)

The equilibrium denaturation of human insulin in a monomer-inducing solvent and of two monomeric insulin analogs, lysB28proB29 insulin and aspB10desB28-30 insulin, was reexamined [Brems, D. N., Brown, P. L., Heckenlaible, L. A., & Frank, B. H. (1990) Biochemistry 29,9289-9293] by circular dichroism (CD) at additional wavelengths in the near-UV region. Previous denaturation studies were limited by the solubility of guanidine hydrochloride being only slightly greater than the level of denaturant required to fully unfold human insulin; therefore, only a few data points were available for construction of the post-transitional baseline. In the present study, we report the use of an unfolded mimic created by enzymatic digestion of insulin to confirm the slope of the post-transitional baseline. Evidence for equilibrium unfolding intermediates for each of these insulins was indicated by noncoincidence of the denaturation transitions as monitored by tyrosine and helical-dependent CD bands (270 and 224 nm, respectively). Additional evidence for intermediates through multiphasic denaturation transitions was obtained at a wavelength likely related to disulfide conformation, 251 nm. The results suggest that for each of the insulins, at least two intermediates are significantly populated. An unfolding model is proposed in which the conformation of the least stable intermediate is slightly unfolded only in the C-terminal segment of the B chain. A second more stable intermediate retains minimal secondary structure while containing localized structure proximal to one or more of the disulfide groups. The presence of equilibrium intermediates has important implications for the folding pathway of insulin, in pharmaceutical applications such as formulation stability, and for conformational transitions that accompany receptor binding.