gebhart/patrepeval huggingface dataset:
Treatment of Steroid Resistant Grade II to IV Acute Gvhd by Infusion of Mesenchymal Stroma Cells Expanded with Human Plasma and Platelet Lysate - a Phase I/II Study (2011)

Abstract Abstract 3046 Introduction For numerous malignant and non-malignant hematological diseases allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative therapy. However, a major complication is the acute graft versus host disease (aGVHD), which is life-threatening and substantially reduces efficacy of HSCT. In particular, the outcome for patients with severe steroid-resistant aGVHD is very poor. Therefore, it remains important to search for new therapeutic strategies for the treatment of aGVHD. Objective Feasibility of the generation mesenchymal stroma cells (MSCs) expanded with human plasma and platelet lysate (hPPL) was tested as well as the feasibility and safety of the application of MSCs in patients with steroid-refractory extensive aGVHD. Method In an open-label, non-randomized prospective phase I/II study MSCs were extracted from the bone marrow of healthy volunteers, expanded with human plasma and platelet lysate (hPPL), and stored. Patients with steroid-refractory extensive aGVHD were treated with ∼2×106/kg MSC. Response rate, transplantation-related deaths, and other adverse events were assessed for up to 12 months after the last infusion of the cells. Results Between January 2009 and December 2010, 18 patients were treated, 5 children and 13 adults, median age was 32.5 years (range 1.3–65.9). Organ involvement of the aGVHD was 67% skin, 83% gastro-intestinal and 28% liver. Overall grade was II for 4 (22%), III for 13 (72%), and IV for 1(6%) patients. 1 patient received one infusion, all other patients received two or more infusions. No patient had side-effects during or immediately after infusions of the MSC. Median follow-up was 5.5 months (range 0.33–12). Complete overall response was observed in 11 (61%) patients after a median of 65 days (range 10–184 days). The overall survival was significant better (p &lt;0.001) compared to non-responders. Of the 11 patients who reached a CR, 8 relapsed median 59 days (1–244) after reaching CR. Three children with subsequently limited cGVHD, allo immune lung and auto-immune cytopenia and 5 adults with all relapse GVHD of the gut, median 98 days (35–302 days). However, GVHD of the gut was then sensitive for the treatment with steroids. Overall, 7 patients died, 4 due to progression of aGVHD, 1 patient due to abdominal bleeding and 2 due to sepsis. Conclusion Generation and infusion of MSCs in steroid-resistant aGVHD grade II- IV is a feasible, safe and very effective. In addition, also patients who initially responded to MSCs but develop later a relapse of aGVHD during tapering or cessation of immunosuppressive drugs become again sensitive to the treatment with steroids. Disclosures: No relevant conflicts of interest to declare.
Assembly of transducer array using anisotropic conductive film for medical imaging applications (2015)

Interconnection technology based on anisotropic conductive film (ACF) has been selected to assemble a transducer array on a flexible substrate in ultrasound imaging applications. The process of bonding and subsequently dicing a transducer on a flexible substrate was evaluated. The results show good integrity of ACF interconnects in test samples undergoing the assembly process. The interconnects, composed of a transducer element and a flex pad, retain high mechanical shear strength and low electrical resistance even after the tough dicing process. Furthermore, a high process yield promising for implementation in industry has been obtained. This work has demonstrated the feasibility of using ACF for assembling ultrasound transducers on system substrates.
Single cell proteomics of tumor compartments identifies differential kinase activities defining sensitivity to mTOR-PI3-kinase inhibition (2021)

ABSTRACT Cancer therapy often results in heterogeneous responses in different metastatic lesions in the same patient. Inter- and intra-tumor heterogeneity in proteomic signaling within the various tumor compartments and its impact on therapy are not well characterized due to the limited sensitivity of single cell proteomic approaches. To overcome this barrier, we applied single cell mass cytometry with a customized 29-antibody panel [against cell states, receptor tyrosine kinases (RTK) and phosphoinositide 3-kinase/mammalian target of rapamycin (PI3K/mTOR)-, mitogen-activated protein kinase (MAPK)-, and cytokine-signaling] to PTEN-deleted orthotopic prostate cancer xenograft models to measure the evolution of kinase activities in different tumor compartments during metastasis and upon drug treatment. Compared with primary tumors and circulating tumor cells (CTCs), bone metastases but not lung and liver metastases exhibited elevated PI3K/mTOR signaling and RTKs including c-Met protein, which, when suppressed, impaired tumor growth in the bone. Intra-tumoral heterogeneity within tumor compartments also arises from highly proliferative EpCAM high epithelial cells with increased PI3K and mTOR kinase activities co-existing with poorly proliferating EpCAM low mesenchymal populations with reduced kinase activities, findings recapitulated in epithelial and mesenchymal CTC populations in metastatic prostate and breast cancer patients. Increased kinase activity in EpCAM high cells rendered them more sensitive to PI3K/mTOR inhibition and drug resistant EpCAM low populations with reduced kinase activity emerged over time. Taken together, single cell proteomics identified microenvironment- and cell state-dependent activation of kinase networks creating heterogeneity and differential drug sensitivity among and within tumor populations across different sites, defining a new paradigm of drug responses to kinase inhibitors.
Toward Integration of Comparative Genetic, Physical, Diversity, and Cytomolecular Maps for Grasses and Grains, Using the Sorghum Genome as a Foundation (2001)

The small genome of sorghum (Sorghum bicolor L. Moench.) provides an important template for study of closely related large-genome crops such as maize (Zea mays) and sugarcane (Saccharum spp.), and is a logical complement to distantly related rice (Oryza sativa) as a "grass genome model." Using a high-density RFLP map as a framework, a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups. By taking advantage of allelic variation revealed by heterologous probes, the positions of corresponding loci on the wheat (Triticum aestivum), rice, maize, sugarcane, and Arabidopsis genomes are being interpolated on the sorghum physical map. Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs; the emerging rice physical map and assembled sequence will further accelerate progress. An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity. "Diversity maps," which depict the levels and patterns of variation in different gene pools, shed light on relationships of allelic diversity with chromosome organization, and suggest possible locations of genomic regions that are under selection due to major gene effects (some of which may be revealed by quantitative trait locus mapping). Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA-progress in cytology promises to provide a means to elucidate such relationships. We seek to provide a detailed picture of the structure, function, and evolution of the genome of sorghum and its relatives, together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis.
Fertilization and early embryology: Comparison of pyruvate uptake by embryos derived from conception and non-conception natural cycles (1994)

The uptake of pyruvate by human embryos derived from natural cycles in the first 24 h following fertilization was examined. Since only one egg was obtained and therefore only one embryo transferred to the woman, it was possible to relate pyruvate consumption by a particular embryo to the outcome of that cycle (pregnancy or no pregnancy). The results showed that embryos have a wide range of pyruvate uptake values (2-53 pmol/embryo/h) but that this variation was reduced significantly to an intermediate range of values in those embryos that were able to implant (10-30 pmol/embryo/h). An association was found between embryo morphology and pyruvate consumption. Morphologically good embryos were more likely to implant if they demonstrated an intermediate pyruvate uptake. However, poor embryos did not implant even if they had a pyruvate uptake of 10-30 pmol/embryo/h. No relationship was found between the type of infertility and pyruvate consumption of individual embryos. It is suggested that the ability of an embryo to implant is multifactorial and that both morphology and pyruvate uptake may be factors.
Glass formation in simple ionic systems via constant pressure molecular dynamics (1989)

The utility of constant pressure molecular dynamics (MD) in studies of glass formation is demonstrated by choosing NaCl and ZnCl2 as examples of MX and MX2 salts. Rigid ion pair potentials have been used to model the two salts. Results of these simulations are in good agreement with general glass formation principles. The effect of the interatomic potential on the glass transition and the cooling rate on glass formation in both the salts is reported. The parameter characterizing the inertia of the borders of the MD simulation cell has a strong influence on the glass transition temperature.
Saturation Effects on Unbalanced Magnetic Pull in a Hydroelectric Generator With an Eccentric Rotor (2007)

We report an investigation of saturation effects on the unbalanced magnetic pull in a hydroelectric generator with 20% static eccentricity. We determine the magnetic pull force by the finite-element method in parallel with a simple analytical model for various no-load voltages and loads. Saturation significantly affects the magnitude of the unbalanced magnetic pull for high voltages and large loads.
Higher Moments of Net-proton Multiplicity Distributions at RHIC (2010)

We report the first measurements of the kurtosis (κ), skewness (S) and variance (σ^2) of net-proton multiplicity (N_p - N_pbar) distributions at midrapidity for Au+Au collisions at \sqrt(s_NN) = 19.6, 62.4, and 200 GeV corresponding to baryon chemical potentials (μ_B) between 200 - 20 MeV. Our measurements of the products κσ^2 and S σ, which can be related to theoretical calculations sensitive to baryon number susceptibilities and long range correlations, are constant as functions of collision centrality. We compare these products with results from lattice QCD and various models without a critical point and study the \sqrt(s_NN) dependence of κσ^2. From the measurements at the three beam energies, we find no evidence for a critical point in the QCD phase diagram for μ_B below 200 MeV.
Synthesis of a Hybrid Nanostructure of ZnO-Decorated MoS2 by Atomic Layer Deposition (2020)

We introduce the synthesis of hybrid nanostructures comprised of ZnO nanocrystals (NCs) decorating nanosheets and nanowires (NWs) of MoS<sub>2</sub> prepared by atomic layer deposition (ALD). The concentration, size, and surface-to-volume ratio of the ZnO NCs can be systematically engineered by controlling both the number of ZnO ALD cycles and the properties of the MoS<sub>2</sub> substrates, which are prepared by sulfurizing ALD MoO<sub>3</sub>. Analysis of the chemical composition combined with electron microscopy and synchrotron X-ray techniques as a function of the number of ZnO ALD cycles, together with the results of quantum chemical calculations, help elucidate the ZnO growth mechanism and its dependence on the properties of the MoS<sub>2</sub> substrate. The defect density and grain size of MoS<sub>2</sub> nanosheets are controlled by the sulfurization temperature of ALD MoO<sub>3</sub>, and the ZnO NCs in turn nucleate selectively at defect sites on MoS<sub>2</sub> surface and enlarge with increasing ALD cycle numbers. At higher ALD cycle numbers, the coalescence of ZnO NCs contributes to an increase in areal coverage and NC size. Additionally, the geometry of the hybrid structures can be tuned by changing the dimensionality of the MoS<sub>2</sub>, by employing vertical NWs of MoS<sub>2</sub> as the substrate for ALD ZnO NCs, which leads to improvement of the relevant surface-to-volume ratio. Such materials are expected to find use in newly expanded applications, especially those such as sensors or photodevices based on a p-n heterojunction which relies on coupling transition-metal dichalcogenides with NCs.
Novel β- and γ-Amino Acid-Derived Inhibitors of Prostate-Specific Membrane Antigen (2020)

Prostate-specific membrane antigen (PSMA) is an excellent biomarker for the early diagnosis of prostate cancer progression and metastasis. The most promising PSMA-targeted agents in the clinical phase are based on the Lys-urea-Glu motif, in which Lys and Glu are α-(l)-amino acids. In this study, we aimed to determine the effect of β- and γ-amino acids in the S1 pocket on the binding affinity for PSMA. We synthesized and evaluated the β- and γ-amino acid analogues with (<i>S</i>)- or (<i>R</i>)-configuration with keeping α-(l)-Glu as the S1'-binding pharmacophore. The structure-activity relationship studies identified that compound <b>13c</b>, a β-amino acid analogue with (<i>R</i>)-configuration, exhibited the most potent PSMA inhibitory activity with an IC<sub>50</sub> value of 3.97 nM. The X-ray crystal structure of PSMA in complex with <b>13c</b> provided a mechanistic basis for the stereochemical preference of PSMA, which can guide the development of future PSMA inhibitors.
Online adaptation of performance maps for centrifugal gas compressors (2014)

This paper investigates the adaptation of different performance maps of centrifugal compressors driven by dual-shaft gas turbines during operation. First the estimation of compressor, gas turbine and combined efficiency are considered. Obtaining performance maps is mainly based on fitting an empirical model to the history of past data together with the understanding of how much new information is contained in newly collected data samples. This amounts to solving a least-squares problem which is formulated as a quadratic program using various constraints. Comparing the actual efficiency to the predicted efficiency by evaluating the previously fitted model, the algorithm decides whether the actual model is accurate enough or a model update is needed. The necessity of having an online model update comes from the fact that the efficiency maps can change due to several factors such as fouling. The algorithm is tested using industrial data from a gas compression station with five gas turbine-driven compressors. The results show the need of online adaptation and that it is possible to accurately predict the different efficiencies using the presented method without excessive model updates. The access to online updated performance maps allows to understand how well the system is performing and gives the opportunity to monitor the efficiency of a specific unit. It is possible to use the adapted performance maps for load sharing optimization with time-varying optimization models.
Controlled Orientation of Cyclodextrin Derivatives Immobilized on Gold Surfaces (1996)

Several different cyclodextrinthiol derivatives have been immobilized on gold surfaces through a chemisorption process to form films which exhibit significantly different features. Three monothiolated cyclodextrin derivatives with different spacers between the cyclodextrin cavity and the thiol group and a mixture of multithiolated cyclodextrins were synthesized and characterized. Chemisorption of these compounds onto gold surfaces gave films which were investigated by Fourier transform infrared (FTIR) spectroscopy, time-of-flight mass spectrometry, contact angle measurements, plasmon surface polariton (PSP) spectroscopy, and cyclic voltammetry. It was found that the chemical structure of each cyclodextrin derivative had a strong influence on the molecular architecture in the resulting films, and in particular on the orientation of the cyclodextrin torus. Models were developed to describe the molecular arrangement in the films.
Latent SHAP: Toward Practical Human-Interpretable Explanations (2022)

Model agnostic feature attribution algorithms (such as SHAP and LIME) are ubiquitous techniques for explaining the decisions of complex classification models, such as deep neural networks. However, since complex classification models produce superior performance when trained on low-level (or encoded) features, in many cases, the explanations generated by these algorithms are neither interpretable nor usable by humans. Methods proposed in recent studies that support the generation of human-interpretable explanations are impractical, because they require a fully invertible transformation function that maps the model's input features to the human-interpretable features. In this work, we introduce Latent SHAP, a black-box feature attribution framework that provides human-interpretable explanations, without the requirement for a fully invertible transformation function. We demonstrate Latent SHAP's effectiveness using (1) a controlled experiment where invertible transformation functions are available, which enables robust quantitative evaluation of our method, and (2) celebrity attractiveness classification (using the CelebA dataset) where invertible transformation functions are not available, which enables thorough qualitative evaluation of our method.
SU‐F‐T‐189: Dosimetric Comparison of Spot‐Scanning Proton Therapy Techniques for Liver Tumors Close to the Skin Surface (2016)

Purpose: Spot‐scanning technique has been utilized to achieve conformal dose distribution to large and complicated tumors. This technique generally does not require patient‐specific devices such as aperture and compensator. The commercially available spot‐scanning proton therapy (SSPT) systems, however, cannot deliver proton beams to the region shallower than 4 g/cm2. Therefore some range compensation device is required to treat superficial tumors with SSPT. This study shows dosimetric comparison of the following treatment techniques: (i) with a tabletop bolus, (ii) with a nozzle‐mounted applicator, and (iii) without any devices and using intensity‐modulated proton therapy (IMPT) technique. Methods: The applicator composed of a combination of a mini‐ridge filter and a range shifter has been manufactured by Hitachi, Ltd., and the tabletop bolus was made by .decimal, Inc. Both devices have been clinically implemented in our facility. Three patients with liver tumors close to the skin surface were examined in this study. Each treatment plan was optimized so that the prescription dose of 76 Gy(RBE) or 66 Gy(RBE) would be delivered to 99% of the clinical target volume in 20 fractions. Three beams were used for tabletop bolus plan and IMPT plan, whereas two beams were used in the applicator plan because the gantry angle available was limited due to potential collision to patient and couch. The normal liver, colon, and skin were considered as organs at risk (OARs). Results: The target heterogeneity index (HI = D 5 /D 95 ) was 1.03 on average in each planning technique. The mean dose to the normal liver was considerably less than 20 Gy(RBE) in all cases. The dose to the skin could be reduced by 20 Gy(RBE) on average in the IMPT plan compared to the applicator plan. Conclusion: It has been confirmed that all treatment techniques met the dosimetric criteria for the OARs and could be implemented clinically.
Effects of degradation on the performance of a triphenylene based liquid crystal organic semiconductor (2015)

We report on time-of-flight (TOF) hole mobility measurements in an aged discotic columnar liquid crystal, Hexakis(pentyloxy)triphenylene (HAT5). The experimental data was fit to an interfacial trapping model based on Van de Walle’s approximations. The theory accurately reproduces the TOF transients of delayed charge release near the optically excited material/electrode interface. Interfacial trapping appears only in the aged materials, but the bulk mobility is the same as that of the pristine material. We also discuss preliminary results of TOF photocurrent transients of HAT5 exposed to ozone.
Scalable trajectory methods for on-demand analog macromodel extraction (2005)

Trajectory methods sample the state trajectory of a circuit as it simulates in the time domain, and build macromodels by reducing and interpolating among the linearizations created at a suitably spaced subset of the time points visited during training simulations. Unfortunately, moving from simple to industrial circuits requires more extensive training, which creates models too large to interpolate efficiently. To make trajectory methods practical, we describe a scalable interpolation architecture, and the first implementation of a complete trajectory "infrastructure" inside a full SPICE engine. The approach supports arbitrarily large training runs, automatically prunes redundant trajectory samples, supports limited hierarchy, enables incremental macromodel updates, and gives 3-10X speedups for larger circuits.
Diagram method for resolution limit calculation in laser microscopy (2018)

In this work, we study the influence of optical process on the resolution limit of laser microscopy. We formulate the calculation rules of the resolution limits for all types of laser microscopy that employ a variety of optical processes occurring in a sample. By replacing the field with the creation/annihilation operators, we develop a theoretical framework to unify the image-forming formulas that cover all interactions between molecules in the sample and the excitation light including vacuum field. To determine the simple rules for the evaluation of optical resolution, our theoretical framework provides the diagram method that describes linear, nonlinear, coherent, and incoherent optical processes. According to our formulas, the type of optical process decisively influences the resolution limit if no a priori information on the sample exists.
Physiochemical properties of enveloped viruses and arginine dictate inactivation (2021)

Arginine most likely interacts with the lipid membrane to cause inactivation. This is shown by larger viruses being more sensitive to inactivation and expansion of the viral size. The enhancement of arginine inactivation when increased hydrophobic molecules are present or arginine is clustered demonstrates a potential mechanism of how arginine interacts with the lipid membrane.
Double negation and iconicity (2007)

Typological research suggests that double negation - the use of two negative markers to denote one negative meaning - is a popular strategy amongst a wide variety of languages. This paper focuses on two types of double negation. The first type, exemplified by Fr. Je ne chante pas ‘I don’t sing’, consists of a discontinuous sentence negator. The second type consists of a sentence negator and a negative indefinite pronoun or adverb as in I don’t see nothing . Iconicity is in the first type related to the language change known as Jespersen’s Cycle leading towards the double negative structure. The second type is arguably one of two possible strategies to avoid the less iconic use of a negative indefinite pronoun.