gebhart/patrepeval huggingface dataset:
ICE: An Interactive Configuration Explorer for High Dimensional Categorical Parameter Spaces (2019)

There are many applications where users seek to explore the impact of the settings of several categorical variables with respect to one dependent numerical variable. For example, a computer systems analyst might want to study how the type of file system or storage device affects system performance. A usual choice is the method of Parallel Sets designed to visualize multivariate categorical variables, However, we found that the magnitude of the parameter impacts on the numerical variable cannot be easily observed here. We also attempted a dimension reduction approach based on Multiple Correspondence Analysis but found that the SVD-generated 2D layout resulted in a loss of information. We hence propose a novel approach, the Interactive Configuration Explorer (ICE), which directly addresses the need of analysts to learn how the dependent numerical variable is affected by the parameter settings given multiple optimization objectives. No information is lost as ICE shows the complete distribution and statistics of the dependent variable in context with each categorical variable. Analysts can interactively filter the variables to optimize for certain goals such as achieving a system with maximum performance, low variance, etc. Our system was developed in tight collaboration with a group of systems performance researchers and its final effectiveness was evaluated with expert interviews, a comparative user study, and two case studies.
A robust optimization methodology for preliminary aircraft design (2015)

This article focuses on a robust optimization of an aircraft preliminary design under operational constraints. According to engineers' know-how, the aircraft preliminary design problem can be modelled as an uncertain optimization problem whose objective (the cost or the fuel consumption) is almost affine, and whose constraints are convex. It is shown that this uncertain optimization problem can be approximated in a conservative manner by an uncertain linear optimization program, which enables the use of the techniques of robust linear programming of Ben-Tal, El Ghaoui, and Nemirovski [Robust Optimization, Princeton University Press, 2009]. This methodology is then applied to two real cases of aircraft design and numerical results are presented.
Bacterial contamination of platelet components: potential solutions to prevent transfusion-related sepsis (2011)

Bacterial contamination of platelet components (PC) is the most prevalent risk for transfusion-transmitted infection. Based on the recent studies with optimal culture methods of expired PC, the prevalence of bacterial contamination is estimated to occur in approximately one in 750 to one in 1000 PC. Only within the last few years have the magnitude of the risks and the range of clinical outcomes associated with bacterial contamination been extensively characterized. Despite increased recognition of bacterial contamination of PC, transfusion-related sepsis is infrequently reported. This has largely been attributed to passive reporting systems, and low levels of clinical awareness for transfusion-related sepsis by primary care physicians. The risk for transfusion of contaminated PC has generally been characterized per component. Importantly, because patients require repeated transfusions of PC during a period of transfusion-dependent thrombocytopenia, it is appropriate to express the risk to receive a contaminated PC on a patient exposure basis. Assuming that the average hematology oncology patient may receive seven PC during a 28-day period of support, the risk of exposure to a contaminated PC is in the range of one in 150 per patient. This level of risk would not be acceptable for other intravenous medications. With increased appreciation of the risk of bacterial contamination, methods were developed to limit the risk of transfusion-transmitted bacteremia. This article focuses on those interventions that have been implemented in routine practice. The most important methods employed to mitigate the risk are improved skin disinfection, initial blood draw diversion, bacterial detection and pathogen inactivation/reduction. These technologies are now undergoing increased use in the clinical practice of transfusion medicine. With increased use, additional data are being generated to more fully characterize the effects of these interventions. Improved disinfection, blood diversion and bacterial detection have decreased, but not resolved the risk of bacterial contamination. Pathogen inactivation/reduction offers the potential for a further substantial decrease of the risk for transfusion of PC contaminated with bacteria.
Seroincidence of Influenza Among HIV-infected and HIV-uninfected Men During the 2009 H1N1 Influenza Pandemic, Bangkok, Thailand (2014)

Among 368 Thai men who have sex with men with paired serum samples collected before and during the 2009 H1N1 influenza pandemic, we determined influenza A (H1N1)pdm09 seroconversion rates (≥4-fold rise in antibody titers by hemagglutination inhibition or microneutralization assays). Overall, 66 of 232 (28%) participants seroconverted after the first year of A(H1N1)pdm09 activity, and 83 of 234 (35%) participants seroconverted after the second year. Influenza A(H1N1)pdm09 seroconversion did not differ between human immunodeficiency virus (HIV)-infected (55 of 2157 [35%]) and HIV-uninfected (71 of 2211 [34%]) participants (P = .78). Influenza A(H1N1)pdm09 seroconversion occurred in approximately one third of our Thai study population and was similar among HIV-infected and HIV-uninfected participants.
T Cell Responses to SARS-CoV-2 (2023)

A large body of evidence generated in the last two and a half years addresses the roles of T cells in SARS-CoV-2 infection and following vaccination. Infection or vaccination induces multi-epitope CD4 and CD8 T cell responses with polyfunctionality. Early T cell responses have been associated with mild COVID-19 outcomes. In concert with animal model data, these results suggest that while antibody responses are key to prevent infection, T cell responses may also play valuable roles in reducing disease severity and controlling infection. T cell memory after vaccination is sustained for at least six months. While neutralizing antibody responses are impacted by SARS-CoV-2 variants, most CD4 and CD8 T cell responses are preserved. This review highlights the extensive progress made, and the data and knowledge gaps that remain, in our understanding of T cell responses to SARS-CoV-2 and COVID-19 vaccines.
Growth Mechanism for Single- and Multi-Layer MoS<sub>2</sub>Nanocrystals (2014)

Transmission electron microscopy (TEM) is used to study growth of MoS2 nanocrystals in situ. The nanocrystals are formed from a submonolayer molybdenum oxide dispersed on an oxide support by sulfidation in an H2S/H2 atmosphere. From series of time-resolved TEM images, it is revealed that single-layer MoS2 nanocrystals form preferentially and that multi-layer nanocrystals form late in the sulfidation process. The TEM images pinpoint that step sites in the support can act as nucleation centers for single-layer nanocrystals and that single-layer nanocrystals grow along the support surface. Moreover, the TEM images reveal that multi-layer MoS2 nanocrystals form in a layer-by-layer mode by the homogeneous nucleation of additional MoS2 layers onto already formed single-layer MoS2 nanocrystals. Hereby, the atomic-scale observations suggest that the formation of multi-layer MoS2 nanocrystals is an energetically more activated process than growth of single-layers. These findings explain why process parameters, such as temperature, can tune the relative fraction of single- to multi-layer MoS2 nanocrystals, which is important for their use in, e.g., hydrotreating catalysis.
Documenting the Research Through Design Process (2016)

Documentation of Research through Design (RtD) processes is essential for capturing and translating design knowledge into broader academic knowledge. Moreover, it can support both design and research objectives internally in RtD projects, as well as external concerns such as project management, knowledge dissemination, and education. In spite of this, RtD documentation has received little sustained attention in prior work. Building on what prior work there is as well as an in-depth analysis of two markedly different cases, we present a framework for planning and evaluating RtD documentation. The framework addresses three core concerns: the medium of documentation, the performativity of documentation, and providing equal support for both research and design.
CoFe<sub>2</sub>O<sub>4</sub>−TiO<sub>2</sub> and CoFe<sub>2</sub>O<sub>4</sub>−ZnO Thin Film Nanostructures Elaborated from Colloidal Chemistry and Atomic Layer Deposition (2010)

CoFe(2)O(4)-TiO(2) and CoFe(2)O(4)-ZnO nanoparticles/film composites were prepared from directed assembly of colloidal CoFe(2)O(4) in a Langmuir-Blodgett monolayer and atomic layer deposition (ALD) of an oxide (TiO(2) or ZnO). The combination of these two methods permits the use of well-defined nanoparticles from colloidal chemistry, their assembly on a large scale, and the control over the interface between a ferrimagnetic material (CoFe(2)O(4)) and a semiconductor (TiO(2) or ZnO). Using this approach, architectures can be assembled with a precise control from the Angstrom scale (ALD) to the micrometer scale (Langmuir-Blodgett film). The resulting heterostructures present well-calibrated thicknesses. Electron microscopy and magnetic measurement studies give evidence that the size of the nanoparticles and their intrinsic magnetic properties are not altered by the various steps involved in the synthesis process. Therefore, the approach is suitable to obtain a layered composite with a quasi-monodisperse layer of ferrimagnetic nanoparticles embedded in an ultrathin film of semiconducting material.
Topology Aware Hybrid Channel Access using Virtual MIMO (2007)

We propose the topology-aware hybrid channel access using virtual MIMO protocol (THAMP). In THAMP, nodes build the channel schedule in a distributed fashion based on the topology information and utilize different antenna gains of virtual MIMO links. Through the joint utilization of spatial diversity gain and spatial multiplexing gain at different nodes, THAMP increases the spatial reuse of the system and reduces the possible collisions of control packets. Simulation results show that THAMP can achieve a better performance than a contention-based MAC protocol using MIMO links.
Effect of high concentration of Co (II) on <b> <i>Enterobacter liquefaciens</i> </b> strain C‐1: A bacterium highly resistant to heavy metals with an unknown genome. (2004)

Heavy metals are required as nutrients for essential functions in microorganisms. However, higher concentrations of these cations are generally toxic and may produce contrasting effects on living organisms. Enterobacter liquefaciens strain C-1, a bacterium isolated from the Moa mine in Cuba, is able to survive in the presence of high concentrations of heavy metals. The proteomes of Enterobacter liquefaciens strain C-1, grown under aerobic conditions in the presence and absence of Co (II) were compared using two-dimensional gel electrophoresis analysis in the isoelectric point range of 4-7 and the mass range of 15-120 kDa. Significant changes in the expression level (> two-fold) were detected for 13 spots: seven and six were up- and down-regulated, respectively. Because the genome of this bacterium is unknown, identification by peptide mass fingerprinting only succeeded in four cases and most of the cross-species identifications were supported by de novo sequencing of tryptic peptides followed by sequence alignment using the MS BLAST program. Twelve different proteins were identified, ten are involved in cellular antioxidant defence probably induced by the presence of Co (II). This is the first step towards understanding the role of proteins participating in the mechanism of resistance to heavy metals in this bacterium.
A 2D/3D hybrid PET scanner with rotating partial slice-septa and its quantitative procedures (2000)

This paper presents a PET scanner capable of acquiring projection data in three-dimensional (3D) and two-dimensional (2D) modes simultaneously. The scanner has rotating partial slice-septa, and coincidence events are stored as 2D data or as 3D data depending on whether the lines of response are collimated by the septa or not. 68Ge/Ga rod sources can be set on the rotating septa, and a transmission scan for attenuation correction is performed in the 2D mode. The scanner allows simultaneous 3D-emission/2D-transmission scanning or post-injection transmission scanning with little cross-talk. A blank scan for detector normalization is also performed with the rotating rod sources in the 2D mode, from which we can derive the normalizing factors in both modes. The 3D/2D difference method is available for scatter correction, even in a dynamic study where the source distribution is changing. A 'summation method' is proposed as a new image reconstruction algorithm, in which the high- and low-frequency components of images are reconstructed from the 3D and 2D data respectively. In this method, most of the scatter contribution in the 3D data is removed by high-pass filtering, not by subtracting estimated scatter distribution, and hence the method is expected to be robust for scatter from outside the axial field of view. Computer simulations revealed that the rotating partial septa offer a single-scatter to true ratio similar to that of the conventional full septa if the depth of the partial septa is properly lengthened, with a small increase in multiple scattering.
Supplemental Figure 2 from Gp96-Ig/Costimulator (OX40L, ICOSL, or 4-1BBL) Combination Vaccine Improves T-cell Priming and Enhances Immunity, Memory, and Tumor Elimination (2023)

&lt;p&gt;Supplemental Figure 2 provides the molecular characterization of all vaccine cell lines used in this manuscript.&lt;/p&gt;
Intermittent hypoxia and hypercapnia induce pulmonary artery atherosclerosis and ventricular dysfunction in low density lipoprotein receptor deficient mice (2013)

Patients with obstructive sleep apnea, who experience episodic hypoxia and hypercapnia during sleep, often demonstrate increased inflammation, oxidative stress, and dyslipidemia. We hypothesized that sleep apnea patients would be predisposed to the development of atherosclerosis. To dissect the mechanisms involved, we developed an animal model in mice whereby we expose mice to intermittent hypoxia/hypercapnia (IHH) in normobaric environments. Two- to three-month-old low-density lipoprotein receptor deficient (Ldlr(-/-)) mice were fed a high-fat diet for 8 or 16 wk while being exposed to IHH for either 10 h/day or 24 h/day. Plasma lipid levels, pulmonary artery and aortic atherosclerotic lesions, and cardiac function were then assayed. Surprisingly, atherosclerosis in the aorta of IHH mice was similar compared with controls. However, in IHH mice, atherosclerosis was markedly increased in the trunk and proximal branches of the pulmonary artery of exposed mice; even though plasma cholesterol and triglycerides were lower than in controls. Hemodynamic analysis revealed that right ventricular maximum pressure and isovolumic relaxation constant were significantly increased in IHH exposed mice and left ventricular % fractional shortening was reduced. In conclusion, 1) Intermittent hypoxia/hypercapnia remarkably accelerated atherosclerotic lesions in the pulmonary artery of Ldlr(-/-) mice and 2) increased lesion formation in the pulmonary artery was associated with right and left ventricular dysfunction. These findings raise the possibility that patients with obstructive sleep apnea may be susceptible to atherosclerotic disease in the pulmonary vasculature, an observation that has not been previously recognized.
Skyrmion Dynamics in Concentric and Eccentric Nano-Ring Structures (2021)

Skyrmions are found to be promising for next-generation energy-efficient spintronic applications. Moreover, ultrafast skyrmion dynamics in gigahertz-band offer an excellent opportunity to exploit such topologically protected nanostructures in high-frequency applications. Here, we present a systematic investigation of the microwave properties of the skyrmions in concentric and eccentric ring structures using micromagnetic simulations. Two gyrotropic modes with clockwise and counterclockwise gyration are observed in skyrmion when excited by an in-plane microwave field. The high-frequency response is found to be enhanced by 3.5 GHz by using a small bias field of 40 mT. The skyrmion dynamics are found to be extremely sensitive to the edge repulsions and a remarkably large frequency shift of 2 GHz of the skyrmion resonance modes is observed by simply varying the position of a skyrmion in an eccentric ring structure. The results are substantiated by directly correlating the observations with inertial mass associated with a skyrmion calculated analytically. The results provide an additional functionality of the skyrmions based on their tunable microwave properties which may have potential implications in the field of miniaturized reconfigurable microwave devices.
ChemInform Abstract: INFRARED STUDY OF SODA‐LIME GLASS DURING HYDRATION AND DEHYDRATION (1983)

Abstract Bei den 2 untersuchten Laboratoriumsgläsern mit 23 (mol‐%) Na 2 O, 5 CaO, 72 SiOz bzw. 15 Na 2 O, 10 CaO, 75 SiO 2 stieg die Höhe der OH‐ und H 2 O‐Banden proportional zur Quadratwurzel der Hydratationszeit.
Long Term Follow-up of a Transjugular Intrahepatic Portosystemic Shunt: A Comparison of Covered and Uncovered Stents (2009)

Purpose: To evaluate the long term patency of transjugular intrahepatic portosystemic shunts (TIPS) and to compare the patency rate of covered and uncovered stents in TIPS. Materials and Methods: The study population included 78 patients with portal hypertension that underwent TIPS between January 1999 and July 2007 at our institution using uncovered stents in 53 patients and covered stents in 25 patients. The primary and secondary patency rates of TIPS were estimated to compare the uncovered and covered stent groups. Results: The primary and secondary patency rates of the TIPS patients were found to be 83.9% and 93.9% at the 6 month follow-up and 73.5% and 88.5% at the12 month follow-up for uncovered and covered stents, respectively. A breakdown patency rates for the 12 month follow-up revealed that the primary patency rates were 76.6% and 66.3% for uncovered and covered stents, respectively; whereas, the secondary patency rates were 94.3% and 73.8% for the uncovered and covered stents, respectively. A comparative analysis did not provide evidence to suggest that a difference exists between the patency rates of the uncovered and covered stent groups (p>0.05). Conclusion: No significant difference was found between the patency rates of the uncovered and covered stent groups. A follow-up to this study would be a more thorough randomized evaluation of the different types of covered stents to compare long-term patency rates.
Efficient Plan Formulation and Organization for Robotic Assemblies and Intelligent Robotic Systems (1990)

An efficient planning technique for the organization and formulation of complete plans applicable to both Robotic Assemblies and Intelligent Robotic Systems is proposed. Constraints are introduced to facilitate and optimize the organizer operations. An example demonstrates the feasibility and applicability of the proposed methodology.
CO/sub 2/ laser sustained CW discharge atomic beam source (1986)

A high pressure, supersonic, laser sustained plasma nozzle beam source has been developed for the production of intense (>10/sup 19/ particles s/sup 1/-sr/sup -1/) beams of atomic and/or radical species having kinetic energies in the range of 1 to 10 eV. A high plasma temperature (10 to 30,000 K) is produced in the throat of a hydrodynamic expansion nozzle by sustaining a cw optical discharge in a gas using a high power cw CO/sub 2/ laser. Gas mixtures are expanded through the nozzle/discharge region creating energetic atoms and molecules. An oxygen atom beam has been produced with a kinetic energy of 2 to 3 eV and an intensity of approx. 10/sup 18/ O-atoms s/sup -1/sr/sup -1/. O-atom collisions (1 eV) from an uncharacterized nickel surface shows strong specular scattering with approximately 50% energy loss to the surface. Argon beams having kinetic energies between 5 to 10 eV with intensities of >10/sup 19/ atoms s/sup -1/sr/sup -1/ have also been produced. 13 refs., 8 figs.
Clinical significance of circulating miR-25-3p as a novel diagnostic and prognostic biomarker in osteosarcoma (2017)

Serum-based circulating miR-25-3p may serve as a non-invasive blood-based biomarker for tumor monitoring and prognostic prediction in osteosarcoma patients.
Notch Inhibition in Cancer: Challenges and Opportunities (2020)

Notch is a key oncogenic pathway in several human cancers and to date, no targeted treatment of Notch activated cancers is available to patients. Therapeutic targeting of Notch has been an unresolved challenge due to severe on-target dose limiting toxicities associated with pan-Notch inhibition by either γ-secretase inhibitors or receptor/ligand targeting MAbs. At Cellestia Biotech, we have identified novel series of small molecule inhibitors of the Notch transcription complex. These molecules act as pan-Notch inhibitors and do not cause toxicities commonly associated with first- and second-generation Notch inhibitors currently tested in the clinic, thus providing a novel and unique opportunity to address a high unmet medical need. Our lead molecule, CB-103 is currently being investigated in Phase-1 dose escalation in cancer patients. Cellestia Biothech is further expanding its medicinal chemistry activities advancing the development of novel molecules for targeting transcription factors in cancer as well as non-cancer indications.
Bradykinin- and thrombin-induced increases in endothelial permeability occur independently of phospholipase C but require protein kinase C activation (1997)

We determined whether activation of phosphatidylinositol-specific phospholipase C (PI-PLC) and a subsequent increase in cytosolic calcium concentration ([Ca2+]i) was an obligatory signaling event mediating the increase in transendothelial permeability induced by bradykinin (BK) and alpha-thrombin (alpha-T). Both BK and alpha-T (each at a concentration range of 0.01-1 microM) caused dose-dependent increases in transendothelial 125I-albumin permeability in cultured bovine pulmonary artery endothelial cell monolayers. Both agonists also produced a rise in inositol (1,4,5)-trisphosphate [Ins(1,4,5)P3] by 10 sec that was followed by a prolonged increase in [Ca2+]i. Pretreatment of endothelial cells with the PLC inhibitor, 1-(6-((17 beta-3-methoxyestra-1,3,5(10)-trien-17-yl)amino)hexyl)-1 H-pyrrole-2,5-dion [(U73122) at 10 microM for 15 min], prevented the increases in Ins(1,4,5)P3 and [Ca2+]i induced by both BK and alpha-T. However, inhibition of PLC with U73122 or another PLC inhibitor, neomycin, did not prevent the increase in endothelial permeability induced by either agonist. In contrast, depletion of cellular protein kinase C (PKC) with phorbol-12-myristate 13-acetate (0.01 microM for 20 hr) increased both BK- and alpha-T-induced phosphoinositide turnover but inhibited the agonist-induced increase in permeability. A PKC inhibitor, staurosporine (5 microM) likewise inhibited the BK-induced increase in endothelial cell permeability to albumin. We conclude that increases in endothelial permeability induced by the inflammatory mediators, BK and thrombin, can occur independently of PLC activation and increased [Ca2+]i but that a PKC-dependent pathway is required for the permeability response.