gebhart/patrepeval huggingface dataset:
Results of a phase I study of bendamustine in combination with ofatumumab, carboplatin, and etoposide (BOCE) for refractory or relapsed aggressive B-cell non-Hodgkin lymphomas (NHL). (2014)

8556 Background: No salvage regimen has shown clear superiority in relapsed NHL. Bendamustine has single agent activity in relapsed aggressive NHL. We conducted a phase I trial using a novel RICE-like salvage regimen in which ofatumumab was substituted for rituximab and bendamustine replaced ifosfamide, combined with carboplatin and etoposide (BOCE) Methods: Patients (pts) with relapsed or refractory aggressive B NHL were eligible. The design was a standard 3+3 design using escalating doses of bendamustine [70, 90, and 120 mg/m2 D1-2] with ofatumumab (cycle 1: 300 mg D1, 1000 mg D3, cycle 2 and 3: 1000 mg D1), carboplatin AUC 5 D2 and etoposide 100mg/m2 D1-3. Results: Eleven pts were enrolled (7M/4F). Median age was 62 (range 53-75), 5 pts (45%) had diffuse large B NHL, 4 pts (36%) had grade 3 follicular NHL, 1 pt (9%) had mantle cell NHL, and 1 pt (9%) had transformed CLL. Five pts (46%) had refractory disease and 6 pts (56%) had relapsed disease. All pts with refractory disease were refractory to rituximab. All pts had stage III or IV disease. sAAIPI was: low-int 55%, high-int 36%, high risk 9%. ORR was 64% [CR: 5 pts (46%); PR: 2 pts (18%)]. Two pts (18%) had progressive disease and 1 pt (9%) had stable disease. Five pts (46%) subsequently underwent an allogeneic transplant. Four pts (36%) died, all of progressive disease. After a median follow-up of 6 months, the estimated 12-months OS is 63.5% DLT was not reached. Grade III-IV toxicity included neutropenia (82%), thrombocytopenia (64%), anemia (64%), lymphopenia (27%), febrile neutropenia (27%), hyponatremia (18%), and hypophosphatemia (18%). Six serious adverse events were reported in 4 pts including acute kidney injury, urinary tract infection, pleural effusion, GI bleeding, thromboembolic event and febrile Infusion related reactions occurred in 27% of pts (all grade I-II). Conclusions: The BOCE regimen is well tolerated in pts with relapsed or refractory aggressive NHL. A phase II trial with bendamustine at the dose of 120mg/m2 is ongoing. The advantage of this regimen over other commonly used salvage strategies is that it can be administered safely in the outpatient setting. Clinical trial information: NCT01458366.
Fragmentation of urinary calculi with 480nm wavelength pulsed dye laser and effct of shock wave amplification by using colored perfusate (1991)

We developed a laserlithotriptor by selecting a 480nm wavelength (WV) laser beam. The 480nm WV laser, when irradiated, generated larger shock wave than the 504nm WV laser since it is absorbed by urinary stones better than the 504nm WV laser which is already in clinical use.Shock wave generated with 480nm WV laser irradiation was amplified significantly by placing the calcium oxalate stone in water colored with indigo carmine or phenolsulphonphtalein (PSP). Shock wave was amplified an average of about 1.5 times in the indigo calamine solution which was added to water in a 1 to 400 ratio compared with the shock wave resulting from irradiation in indigo-free water. When the dilution rate was 1 to 200, shock wave was amplified an average of 1.79 times. In PSP added water with a 1 to 100 ratio, shock wave amplification was enhanced an average of 1.74 times compared to that resulting from irradiation in PSP-free water.This approach might be effective to disintegrate hard stone such as cystine stone without increasing output energy.
Réparation et régénération de l’épithélium respiratoire (2005)

Despite an efficient defence system, the airway surface epithelium, in permanent contact with the external milieu, is frequently injured by inhaled pollutants, microorganisms and viruses. The response of the airway surface epithelium to an acute injury includes a succession of cellular events varying from the loss of the surface epithelium integrity to partial shedding of the epithelium or even to complete denudation of the basement membrane. The epithelium has then to repair and regenerate to restore its functions, through several mechanisms including basal cell spreading and migration, followed by proliferation and differentiation of epithelial cells. The cellular and molecular factors involved in wound repair and epithelial regeneration are closely interacting and imply extracellular matrix proteins, matrix metalloproteinases (MMPs) and their inhibitors as well as cytokines and growth factors secreted by airway epithelial and mesenchymal cells. The development of in vitro and in vivo models of airway epithelium wound repair allowed the study of the spatio-temporal modulation of these factors during the different steps of epithelial repair and regeneration. In this context, several studies have demonstrated that the matrix and secretory environment are markedly involved in these mechanisms and that their dysregulation may induce remodelling of the airway mucosa. A better knowledge of the mechanisms involved in airway epithelium regeneration may pave the way to regenerative therapeutics allowing the reconstitution of a functional airway epithelium in numerous respiratory diseases such as asthma, chronic obstructive pulmonary diseases, cystic fibrosis and bronchiolitis.
Structure-activity relationship studies of novel somatostatin analogs with antitumor activity. (1994)

A series of new somatostatin analogs were synthesized in order to study the relative importance of specific substitutions in relation to selectivity between their endocrine and antitumor effects. Substitutions were carried out in all positions, except for Lys in position 5. Peptides were tested for their ability to inhibit in vitro and in vivo GH release, proliferation of the MCF 7 breast carcinoma cell line and tyrosine kinase activity in the HT 29 human colon carcinoma cell line. Selective biological activity was achieved in GH release and antitumor activity by the different amino acid substitutions. One of the analogs, with a five-residue ring (D-Phe-Cys-Tyr-D-Trp-Lys-Cys-Thr-NH2, TT-232), was unique. It had no GH release inhibitory activity, but did have strong tyrosine kinase inhibitory and antiproliferative effects.
Analyzing cytotoxicity kinetics with a novel automated high-throughput real-time killing assay (P3366) (2013)

Abstract Cytotoxicity is an essential parameter to examine killer cell activity, to screen hits for new drugs, and to proof safety evaluation. Cytotoxicity assays are routinely used in basic research, clinical studies, and industrial applications. However, the most commonly applied standard end-point cytotoxicity assays largely suffer from the lack of kinetic information, which is indispensable to assess killing competence. Here we report a quantitative and highly sensitive calcein-based real-time high-throughput cytotoxicity assay on a single cell level and for population use. By determining fluorescence loss as a function of the fraction of lysed cells, this assay measures the kinetics of cytotoxicity over a broad dynamic range. The high time resolution of the assay also provides kinetic information with the potential to reveal neglected/immeasurable properties in the process of cytotoxicity of both purified human cytotoxic T lymphocytes and natural killer cells. To test its clinical potential, we have also applied this assay to screen the cytotoxic potential of (easy to prepare) peripheral blood mononuclear cells in healthy blood donors. In summary, this assay should substantially increase the screening efficiency for clinical and industrial purposes and offer quantitative kinetic data with a high time resolution.
A Detailed Analysis of the Microstructural Changes in the Vicinity of a Crack-Initiating Defect in Additively Manufactured AISI 316L (2023)

The fatigue life of metals manufactured via laser-based powder bed fusion (L-PBF) highly depends on process-induced defects. In this context, not only the size and geometry of the defect, but also the properties and the microstructure of the surrounding material volume must be considered. In the presented work, the microstructural changes in the vicinity of a crack-initiating defect in a fatigue specimen produced via L-PBF and made of AISI 316L were analyzed in detail. Xenon plasma focused ion beam (Xe-FIB) technique, scanning electron microscopy (SEM), and electron backscatter diffraction (EBSD) were used to investigate the phase distribution, local misorientations, and grain structure, including the crystallographic orientations. These analyses revealed a fine grain structure in the vicinity of the defect, which is arranged in accordance with the melt pool geometry. Besides pronounced cyclic plastic deformation, a deformation-induced transformation of the initial austenitic phase into α’-martensite was observed. The plastic deformation as well as the phase transformation were more pronounced near the border between the defect and the surrounding material volume. However, the extent of the plastic deformation and the deformation-induced phase transformation varies locally in this border region. Although a beneficial effect of certain grain orientations on the phase transformation and plastic deformability was observed, the microstructural changes found cannot solely be explained by the respective crystallographic orientation. These changes are assumed to further depend on the inhomogeneous distribution of the multiaxial stresses beneath the defect as well as the grain morphology.
Toward Wireless Receivers without Crystals Invited Paper (2005)

In new low cost, IOW, bit rate wireless protocols such as ZigbeeTM and BIuetoothTM, there is significant economic motivation to implement transceivers with a completely integrated alternative to quartz crystals. In this paper, we explore a differential detection based method of recovering a direct sequence spread spectrum signal with a receiver that does not have a crystal reference. Despite the additional frequency offset and phase introduced by using an integrated crystaIless reference oscillator, we find that such a receiver is feasible and can perform sufficiently for many applications. Indcr Terms - crystai-less communicstion, differential detection, phase noise.
Antibody development against biologic agents used for the treatment of inflammatory bowel disease and antibody prevention with immunosuppressives (2016)

This is the protocol for a review and there is no abstract. The objectives are as follows: The primary objectives are to systematically review the prevalence of immunogenicity to biologics with the use of different test assays, the impact of ADA formation on the efficacy and safety of biologics and the influence of combination therapy on immunogenicity in patients with IBD.
Thermal annealing effects on SCAATTM substrate grown toward the c- and m-directions (2019)

The effect of the thermal annealing on an acidic ammonothermal gallium nitride (GaN) crystal grown toward the c- and m-directions was investigated. The specific annihilation of hydrogenated Ga vacancies was confirmed for the GaN crystal grown toward the m-direction but not for that grown toward the c-direction. A transparent and yellow luminescence-free ammonothermal GaN substrate was realized. The annihilation of the hydrogenated Ga vacancies was explained by the difference in the diffusion of F incorporated as a mineralizer between the c- and m-directions.
Desmoplastic Trichoepithelioma (2012)

In a 58-year-old woman with blepharospasm, a slowly enlarging left inferomedial eyelid lesion developed. It measured 3 × 5 mm and was nonulcerated, well-circumscribed, whitish, upraised, and firm. An initial incomplete excision followed by a total repeated excision revealed small squamous microcysts, often exhibiting calcifications and cords of nonclefting basaloid cells embedded in a scirrhous stroma characteristic of desmoplastic trichoepithelioma (DTE). Immunohistochemical investigations disclosed CD34-positive stromal fibroblasts and many CK20-positive Merkel cells located among the epithelial cells, features absent in mimicking sclerosing basal cell carcinoma (BCC). The tumor has not recurred during 6 months of follow up. Besides BCC, the differential diagnosis chiefly concerns syringoma and microcystic adnexal carcinoma. Surgical therapy should aim at complete excision but does not have to be as extensive or aggressive as that used for morpheic or sclerosing BCC because of its lack of diffusely infiltrating margins.
Diversity-Promoting Bayesian Learning of Latent Variable Models (2017)

To address three important issues involved in latent variable models (LVMs), including capturing infrequent patterns, achieving small-sized but expressive models and alleviating overfitting, several studies have been devoted to "diversifying" LVMs, which aim at encouraging the components in LVMs to be diverse. Most existing studies fall into a frequentist-style regularization framework, where the components are learned via point estimation. In this paper, we investigate how to "diversify" LVMs in the paradigm of Bayesian learning. We propose two approaches that have complementary advantages. One is to define a diversity-promoting mutual angular prior which assigns larger density to components with larger mutual angles and use this prior to affect the posterior via Bayes' rule. We develop two efficient approximate posterior inference algorithms based on variational inference and MCMC sampling. The other approach is to impose diversity-promoting regularization directly over the post-data distribution of components. We also extend our approach to "diversify" Bayesian nonparametric models where the number of components is infinite. A sampling algorithm based on slice sampling and Hamiltonian Monte Carlo is developed. We apply these methods to "diversify" Bayesian mixture of experts model and infinite latent feature model. Experiments on various datasets demonstrate the effectiveness and efficiency of our methods.
Supplementary Figures from Genomic Landscape of Atypical Adenomatous Hyperplasia Reveals Divergent Modes to Lung Adenocarcinoma (2023)

&lt;p&gt;Figure S1: Mutation burden in atypical adenomatous hyperplasia and lung adenocarcinoma; Figure S2: Mutation burden in atypical adenomatous hyperplasia and lung adenocarcinoma based on tobacco history; Figure S3: Mutations in cancer driver genes in atypical adenomatous hyperplasia and lung adenocarcinoma; Figure S4: Representative validation of somatic mutations by digital PCR.&lt;/p&gt;
Geometric effect in a vertical stack-up metal-insulator-metal tunnel diode (2017)

The geometric effect was investigated in a vertically designed metal-insulator-metal (MIM) tunnel diode for which a narrow tunneling distance can be controlled easily and reliably, with the goal of enhancing rectifying efficiency, based on the angle of a pointed shape electrode and various thicknesses of insulator material. Although MIM tunneling diodes can provide ultra- high working speeds (&amp;gt;THz), the very low contrast ratio between forward and reverse currents results in poor rectifying efficiency. An asymmetric geometry design with two metal electrodes can be an effective approach for enhancing the contrast ratio between the tunneling currents. Using a sharp electrode with a pointed shape, it was determined that the rectifying efficiency and tunneling probability could be increased impressively depending on the angle of the pointed shape of the electrode. Moreover, the selection of insulation material was also important for improving efficiency. Although the band gap of Al2O3 is larger than that of HfO2, the rectifying efficiency was significantly improved by blocking reverse current well. In general, large band gap insulator materials are inappropriate for a tunneling device, due to the low tunneling current. However, in our approach, since the issue of low tunneling probability is compensated by the sharp tip structure, the larger band gap insulator produced better rectifying efficiency with the appropriate current density. The results of this study demonstrated that geometric design could be a possible solution to increase rectifying efficiency. If the geometric effect in the tunneling diode structures will be optimized more, it can improve the applicability of vertical stack-up MIM tunnel diode to THz switching devices, tunneling transistors and ultra-high speed electronics.
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa (2018)

Taken together, these results suggest that the metabolic capabilities of B2 strains vary significantly from those of other strains, enabling B2 strains to colonize intestinal mucosa.The results from this study motivate a broad experimental assessment of the nutritional effects on E. coli B2 pathophysiology in IBD patients.
DFM for defect-free DSA hole shrink process (2014)

Application of the directed self-assembly (DSA) of block copolymer (PS-b-PMMA) to the hole shrink process has gained large attention because of the low cost and the potential for sub-lithographic patterning of contact, via and cut masks (Ref. [1-2] and references therein). In order to realize the DSA hole shrink process for manufacturing, however, one still has to resolve a few critical issues such as morphological defects and placement errors [3]. The morphological defect here indicates the PS residual layer lying between the vertical PMMA cylinder and the substrate, which prevents the PMMA cylinder from touching to the bottom surface. Such underlying defects cannot be observed by conventional approach with the top-down SEM images. In this study, we have utilized a simplified model, so-called the Ohta- Kawasaki (OK) model [4-5] to optimize the DSA hole shrink process. The advantages of the OK model are considerably low computational expense and reasonable accuracy. First, we demonstrated that the OK model could indeed predict complicated, three-dimensional morphologies of the diblock copolymer in the pre-patterned hole. All the results were computed within one minute, and they were reasonably comparable to those obtained from the self-consistent field theory (SCFT) [6]. Then, we calibrated the model parameters with the cross-sectional TEM images, minimizing the errors between the simulated thickness of PS residual layer and the experimental data. The calibrated model was used for the optimization of the guide hole shape and for the exploration of the multi-cylinder case.
ChemInform Abstract: C(5)‐Epimerization in Glycopyranosides During the Cyclization of Anomeric Radicals: Ease of the Intramolecular 1,5‐Hydrogen Atom Transfer. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Thermal modeling and experimental study of 3D stack package with hot spot consideration (2015)

This paper provides a unique approach to thermal modeling of BEOL (Back End Of Line) layers in a 3D stacked LSI and introduces a novel cold plate design method by using a 30 mm by 30 mm LSI as an example. The paper focuses on BEOL thermal characterization, flow rate control in branch-channels and the micro-channels behind them in a cold plate in accordance with a power map of the LSI, and an experimental setup for thermal verification. The power map had several considerable hot spots. The cold plate was able to considerably reduce temperature differences by 5°C all across the top surface of the LSI on the load condition of 120 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for hot spots and 60.5 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for other areas with regard to heat density, at a flow rate of 1 L/min. to the cold plate inlet. It also achieved a low of 5 kPa in pressure loss while the flow rate ratio of hot spots to others was controlled to approximately 5:1.
Group-specific, major histocompatibility complex class I-restricted cytotoxic responses to human immunodeficiency virus 1 (HIV-1) envelope proteins by cloned peripheral blood T cells from an HIV-1-infected individual. (1988)

Freshly separated unfractionated peripheral blood mononuclear cells (PBMC) and cloned cell lines from a healthy human immunodeficiency virus 1 (HIV-1)-seropositive individual were examined for cytotoxic responses to HIV proteins expressed by recombinant vaccinia viruses. It was found that freshly isolated PBMC recognize variant envelope proteins of HIV-1 but not a more distantly related envelope protein derived from the simian immunodeficiency virus (SIVmac). Although the effector cells were predominantly CD8+, both MHC-matched and -unmatched target cells were lysed. Cytotoxic T lymphocyte (CTL) clones were found to lyse cells expressing HIV-1 envelope or reverse transcriptase. In contrast to the cytotoxic response detected with PBMC, the cloned CTLs were major histocompatibility complex (MHC) class I restricted. Our finding that a cloned CTL line lysed cells expressing highly divergent HIV envelopes strongly suggested that a conserved epitope was recognized. Identification of these shared epitopes may assist in designing a vaccine for HIV-1 that could stimulate MHC-restricted cytotoxic responses.