gebhart/patrepeval huggingface dataset:
Application of human pancreatic carcinoid BON cells for receptor-targeted drug development (2010)

In our previous study, we found that several tumor cell lines displayed high receptor-specific binding affinity, one of which, the human pancreatic carcinoid BON cell line, demonstrates high affinity binding of the bombesin (BN) and somatostatin (SST) receptor-specific ligands. In the present study, BON cells, as a representative model, were further applied to evaluate various peptide analogs and cytotoxic receptor-targeted peptide conjugates. We observed quick ligand-receptor internalization in BON cells as well as high binding affinity. Furthermore, BON cells have high expression of multidrug resistance-associated genes (MDR1) and show camptothecin (CPT) resistance. Various receptor-specific cytotoxic conjugates were synthesized and evaluated in the BON cell model via in vitro and in vivo studies. We found that all the tested conjugates displayed potent antitumor ability in xenografts. Especially, the CPT conjugates, CPT-SST, and CPT-BN, are most likely to increase sensitivity to CPT-resistant BON cells. Our findings suggest that appropriately defined tumor cell lines may provide physiologically relevant cell-based evaluations of novel peptide analogs and receptor-targeted chemotherapeutics.
Characterization and Liquid Chromatography-MS/MS Based Quantification of Hydroxylated Fullerenes (2011)

Highly water-soluble hydroxylated fullerene derivatives are being investigated for a wide range of commercial products as well as for potential cytotoxicity. However, no analytical methods are currently available for their quantification at sub-ppm concentrations in environmental matrixes. Here, we report on the development and comparison of liquid chromatography-ultraviolet/visible spectroscopy (LC-UV/vis) and liquid chromatography-mass spectrometry (LC-MS) based detection and quantification methods for commercial fullerols. We achieved good separation efficiency using an amide-type hydrophilic interaction liquid chromatography (HILIC) column (plate number >2000) under isocratic conditions with 90% acetonitrile as the mobile phase. The method detection limits (MDLs) ranged from 42.8 ng/mL (UV detection) to 0.19 pg/mL (using MS with multiple reaction monitoring, MRM). Other MS measurement modes achieved MDLs of 125 pg/mL (single quad scan, Q1) and 1.5 pg/mL (multiple ion monitoring, MI). Each detection method exhibited a good linear response over several orders of magnitude. Moreover, we tested the robustness of these methods in the presence of Suvanee River fulvic acids (SRFA) as an example of organic matter commonly found in environmental water samples. While SRFA significantly interfered with UV- and Q1-based quantifications, the interference was relatively low using MI or MRM (relative error in presence of SRFA: 8.6% and 2.5%, respectively). This first report of a robust MS-based quantification method for modified fullerenes dissolved in water suggests the feasibility of implementing MS techniques more broadly for identification and quantification of fullerols and other water-soluble fullerene derivatives in environmental samples.
Estimating Trait Heritability in Highly Fecund Species (2015)

Increasingly, researchers are interested in estimating the heritability of traits for nonmodel organisms. However, estimating the heritability of these traits presents both experimental and statistical challenges, which typically arise from logistical difficulties associated with rearing large numbers of families independently in the field, a lack of known pedigree, the need to account for group or batch effects, etc. Here we develop both an empirical and computational methodology for estimating the narrow-sense heritability of traits for highly fecund species. Our experimental approach controls for undesirable culturing effects while minimizing culture numbers, increasing feasibility in the field. Our statistical approach accounts for known issues with model-selection by using a permutation test to calculate significance values and includes both fitting and power calculation methods. We further demonstrate that even with moderately high sample-sizes, the p-values derived from asymptotic properties of the likelihood ratio test are overly conservative, thus reducing statistical power. We illustrate our methodology by estimating the narrow-sense heritability for larval settlement, a key life-history trait, in the reef-building coral Orbicella faveolata. The experimental, statistical, and computational methods, along with all of the data from this study, are available in the R package multiDimBio.
Continuous evolution of Ga adlayer coverages during plasma-assisted molecular-beam epitaxy of (0001) GaN (2005)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation G. Koblmüller, J. Brown, R. Averbeck, H. Riechert, P. Pongratz, J. S. Speck; Continuous evolution of Ga adlayer coverages during plasma-assisted molecular-beam epitaxy of (0001) GaN. Appl. Phys. Lett. 24 January 2005; 86 (4): 041908. https://doi.org/10.1063/1.1853530 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioApplied Physics Letters Search Advanced Search |Citation Search
Autologous mixed lymphocyte reaction and postoperative prognosis in patients with gastric carcinoma (1996)

The autologous mixed lymphocyte reaction (AMLR) represents a self recognitive response, which is very important in the immunoregulatory network system. We investigated whether the AMLR activity of patients with gastric carcinoma could reflect the postoperative prognosis to clarify the significance of autoreactivity in anti-tumor immune system in cancer patients. The AMLR activity was suppressed both in the peripheral blood and in the spleen of patients with gastric carcinoma. The patients were divided into two groups; high responder and low responder group. The former consisted of patients whose AMLR activity was extremely suppressed, and the latter of patients whose AMLR activity was mildly suppressed. The survival rate and disease-free survival rate were generally higher in the high responder group than in the low responder group, especially in the spleen. Moreover, none of the patients in the high responder group for the AMLR activity in the spleen died within three years. These results indicated that the AMLR activity could reflect the prognosis of patients who received conventional curative operation. Therefore, it was suggested that the AMLR might be a useful parameter of postoperative prognosis in gastric cancer patients and that autoreactive T cells might play a pivotal role in auto-specific immunological control of tumor growth and metastases.
3PO: Programmed Far-Memory Prefetching for Oblivious Applications (2022)

Using memory located on remote machines, or far memory, as a swap space is a promising approach to meet the increasing memory demands of modern datacenter applications. Operating systems have long relied on prefetchers to mask the increased latency of fetching pages from swap space to main memory. Unfortunately, with traditional prefetching heuristics, performance still degrades when applications use far memory. In this paper we propose a new prefetching technique for far-memory applications. We focus our efforts on memory-intensive, oblivious applications whose memory access patterns are independent of their inputs, such as matrix multiplication. For this class of applications we observe that we can perfectly prefetch pages without relying on heuristics. However, prefetching perfectly without requiring significant application modifications is challenging. In this paper we describe the design and implementation of 3PO, a system that provides pre-planned prefetching for general oblivious applications. We demonstrate that 3PO can accelerate applications, e.g., running them 30-150% faster than with Linux's prefetcher with 20% local memory. We also use 3PO to understand the fundamental software overheads of prefetching in a paging-based system, and the minimum performance penalty that they impose when we run applications under constrained local memory.
Uncertainty Weighted Actor-Critic for Offline Reinforcement Learning (2021)

Offline Reinforcement Learning promises to learn effective policies from previously-collected, static datasets without the need for exploration. However, existing Q-learning and actor-critic based off-policy RL algorithms fail when bootstrapping from out-of-distribution (OOD) actions or states. We hypothesize that a key missing ingredient from the existing methods is a proper treatment of uncertainty in the offline setting. We propose Uncertainty Weighted Actor-Critic (UWAC), an algorithm that detects OOD state-action pairs and down-weights their contribution in the training objectives accordingly. Implementation-wise, we adopt a practical and effective dropout-based uncertainty estimation method that introduces very little overhead over existing RL algorithms. Empirically, we observe that UWAC substantially improves model stability during training. In addition, UWAC out-performs existing offline RL methods on a variety of competitive tasks, and achieves significant performance gains over the state-of-the-art baseline on datasets with sparse demonstrations collected from human experts.
Sortase structure and specificity in streptococci. (2014)

<title>Abstract</title> This chapter reviews currently available data on pilus-specific sortases in streptococci, focusing on their genomic organization, structure, substrate recognition specificity and regulation.
The Hepatocyte as a Household forPlasmodiumParasites (2020)

The liver is well known for its pivotal role in numerous aspects of animal physiology, ranging from detoxification of drugs, toxins, and other harmful substances, to the metabolism of proteins, lipids, carbohydrates, and vitamins, as well as its role in steroidogenesis and bile secretion, among many others. Plasmodium belongs to the phylum Apicomplexa, a taxonomic group of single-celled parasites with characteristic secretory organelles at the apical end of the cell. Sporozoites are the hepatocyte-invasive parasite forms that are transmitted to the vertebrate host by the mosquito bite. Plasmodium parasites are also auxotrophic for certain lipid species and metabolites, such as cholesterol, lipoic acid, and phosphatidylcholine, with deletion of the parasite lipid adenosine triphosphate-binding cassette transporters resulting in liver-stage arrest. In the liver the parasite achieves the highest replication rate of its life cycle, and one of highest rates of replication observed in eukaryotic cells.
Particle Interactions in Dry Powder Inhaler Unit Processes: A Review (2011)

Abstract Recent development and methods of designing and optimizing dry powder formulations have extended the therapeutic potential of inhaled dosage forms. Successful drug delivery as indicated by a high and reproducible fine particle fraction, required to achieve the desired therapeutic effect while minimizing potential toxicity, depends on an understanding of the physico-chemical properties of powder blends, their performance and availability of adequate tools to screen and predict their behavior. The scope of this review includes three important perspectives for inhaled drug delivery: (1) Fundamental aspects of interparticulate interactions of pharmaceutical dry powder aerosols at rest and in resuspension; (2) The influences of pharmaceutical processing including milling, mixing, filling and storage, and their influence on powder dispersion; (3) Current strategies for formulation optimization and methods for in vitro aerosolization performance prediction. Keywords: DRY POWDER INHALERDRY POWDER AEROSOL FORMULATIONINTERPARTICULATE INTERACTIONRESUSPENSIONPHARMACEUTICAL PROCESSINGFORMULATION OPTIMIZATIONPERFORMANCE PREDICTION
Influence of polymer gate dielectrics on n-channel conduction of pentacene-based organic field-effect transistors (2007)

This work elucidates the way polymer gate dielectrics affect the accumulation and transport of charge carriers in the active layer of organic field-effect transistors (OFETs). Incorporating a poly(vinyl alcohol) polymer interfacial film and another cross-linked poly(4-vinyl phenol) layer as a double-layer gate dielectric causes the pentacene-based OFETs to exhibit effective n-channel conduction of a saturated, apparent pinch-off drain-source current with the electron mobility of ∼0.012cm2V−1s−1. The formation of an n channel in the pentacene layer is supported by the increased capacitance that is identified by the quasistatic capacitance-voltage measurements of devices with the metal-insulator-semiconductor configuration, biased at a positive gate voltage, in the n-type accumulation regime.
Chemoimmunotherapy with ofatumumab in combination with CHOP in previously untreated follicular lymphoma (2012)

An international, Phase II trial was conducted to assess two doses of ofatumumab, a human CD20 monoclonal antibody, combined with cyclophosphamide (750 mg/m(2) ), doxorubicin (50 mg/m(2) ), prednisone (100 mg days 3-7) and vincristine (1·4 mg/m(2) ) (O-CHOP), as frontline treatment for follicular lymphoma (FL). 59 patients with previously untreated FL were randomized to ofatumumab 500 mg (n = 29) or 1000 mg (n = 30) day 1, with CHOP on day 3 every 3 weeks for six cycles. Median duration of FL was 0·1 years for both dose groups; 34% and 38% of patients had high-risk Follicular Lymphoma International Prognostic Index (FLIPI) scores in the 500- and 1000-mg dose groups, respectively. Overall response rate was 90% for the 500-mg group and 100% for the 1000-mg group. 62% of patients achieved complete response (CR)/unconfirmed CR (CRu). 76% of patients with FLIPI score 3-5 attained CR/CRu. Longer follow-up time is needed for analysis of survival end points. The most common Common Terminology Criteria grade 3-4 investigator-reported adverse events were leucopenia (29%) and neutropenia (22%). No deaths have been reported. O-CHOP was safe and efficacious in patients with previously untreated FL, including high-risk FLIPI groups. This trial was registered at www.clinicaltrials.gov (NCT00494780).
TiO2-SnO2:F interfacial electronic structure investigated by soft x-ray absorption spectroscopy (2012)

The electronic structure of the titanium dioxide (TiO${}_{2}$)-fluorine-doped tin dioxide (SnO${}_{2}$:F) interface is investigated by soft x-ray absorption spectroscopy using synchrotron radiation. The measurements probe the site- and symmetry-selected unoccupied density of states and reflect the interaction between an early transition-metal-oxide (${d}^{0}$) semiconductor and a post-transition-metal-oxide (${d}^{10}$) degenerate semiconductor. The distinct interfacial electronic structure of TiO${}_{2}$-SnO${}_{2}$:F is established by contrasting spectra with those for anatase and rutile TiO${}_{2}$, SnO${}_{2}$:F, and ZnO-SnO${}_{2}$:F and CdO-SnO${}_{2}$:F interfaces. Oxygen 1$s$ absorption spectra, which relate to the O 2$p$ partial density of states of the conduction band, indicate that the interface is associated with a reduction in Ti $d$-O $p$ orbital hybridization and an alteration of the TiO${}_{2}$ crystal field. These observations are consistent with measured titanium 2$p$ absorption spectra, which in addition provide evidence for distortion of long-range order around the cation site in the interfacial TiO${}_{2}$. The TiO${}_{2}$-SnO${}_{2}$:F interface is a functional component of a number of optoelectronic devices, perhaps most notably within the anode structure of solar cell architectures. In nonequilibrium conditions, such as those found in operating solar cells, interfacial electronic structure directly influences performance by modifying, for instance, the quasi-Fermi level electrons and the potential distribution at the transparent electrode.
Synthesis and in Vitro Evaluation of 4-Substituted N-(1,1-Dimethylethyl)-3-oxo-4-androstene-17.beta.-carboxamides as 5.alpha.-Reductase Inhibitors and Antiandrogens (1995)

4-Substituted N-(1,1-dimethylethyl)-3-oxo-4-androstene-17 beta-carboxamides with the hydroxy (OH) 3d, mercapto (SH) 3e, chloro (Cl) 3f, and bromo (Br) 3g substituents at the 4-position were prepared in a two-step sequence with overall yields of 21%, 27%, 41%, and 37%, respectively. Compounds 3d-g showed weak inhibitory activity on human type I 5 alpha-reductase (IC50 > or = 700 nM) while they had intermediate inhibitory activity on human type II 5 alpha-reductase at IC50S of 172, 437, 192, and 387 nM, respectively. In androgen-sensitive Shionogi cells, the inhibition of dihydrotestosterone (DHT) stimulatory action on the proliferation of the androgen-sensitive cancer cells by all four compounds was high at IC50S of 170-279 nM compared with 117 nM for hydroxyflutamide. The present data show compounds having both moderate inhibition of human type II 5 alpha-reductase activity and relatively potent antiandrogenic action, two beneficial characteristics in the therapy of androgenic-sensitive diseases.
Lifetime measurement of the 1s5metastable state of argon and krypton with a magneto-optical trap (1993)

The natural decay rates of the 1${\mathit{s}}_{5}$[${\mathit{np}}^{5}$(n+1)s${,}^{3}$${\mathit{P}}_{2}$] metastable state of argon and krypton are experimentally determined using a magneto-optical trap. The method to determine the lifetime of a metastable state from a fluorescence decay measurement is described. The obtained lifetimes are ${38}_{\mathrm{\ensuremath{-}}5}^{+8}$ s for argon and ${39}_{\mathrm{\ensuremath{-}}4}^{+5}$ s for krypton.
Proposed conventions for describing germacranolide sesquiterpenes (1972)

D. Rogers, G. P. Moss and S. Neidle, J. Chem. Soc., Chem. Commun., 1972, 142 DOI: 10.1039/C39720000142
Metal Oxide Nanoparticle Growth on Graphene via Chemical Activation with Atomic Oxygen (2013)

Chemically interfacing the inert basal plane of graphene with other materials has limited the development of graphene-based catalysts, composite materials, and devices. Here, we overcome this limitation by chemically activating epitaxial graphene on SiC(0001) using atomic oxygen. Atomic oxygen produces epoxide groups on graphene, which act as reactive nucleation sites for zinc oxide nanoparticle growth using the atomic layer deposition precursor diethyl zinc. In particular, exposure of epoxidized graphene to diethyl zinc abstracts oxygen, creating mobile species that diffuse on the surface to form metal oxide clusters. This mechanism is corroborated with a combination of scanning probe microscopy, Raman spectroscopy, and density functional theory and can likely be generalized to a wide variety of related surface reactions on graphene.
An Integrated Region-, Boundary-, Shape-Based Active Contour for Multiple Object Overlap Resolution in Histological Imagery (2012)

Active contours and active shape models (ASM) have been widely employed in image segmentation. A major limitation of active contours, however, is in their 1) inability to resolve boundaries of intersecting objects and to 2) handle occlusion. Multiple overlapping objects are typically segmented out as a single object. On the other hand, ASMs are limited by point correspondence issues since object landmarks need to be identified across multiple objects for initial object alignment. ASMs are also are constrained in that they can usually only segment a single object in an image. In this paper, we present a novel synergistic boundary and region-based active contour model that incorporates shape priors in a level set formulation with automated initialization based on watershed. We demonstrate an application of these synergistic active contour models using multiple level sets to segment nuclear and glandular structures on digitized histopathology images of breast and prostate biopsy specimens. Unlike previous related approaches, our model is able to resolve object overlap and separate occluded boundaries of multiple objects simultaneously. The energy functional of the active contour is comprised of three terms. The first term is the prior shape term, modeled on the object of interest, thereby constraining the deformation achievable by the active contour. The second term, a boundary-based term detects object boundaries from image gradients. The third term drives the shape prior and the contour towards the object boundary based on region statistics. The results of qualitative and quantitative evaluation on 100 prostate and 14 breast cancer histology images for the task of detecting and segmenting nuclei and lymphocytes reveals that the model easily outperforms two state of the art segmentation schemes (geodesic active contour and Rousson shape-based model) and on average is able to resolve up to 91% of overlapping/occluded structures in the images.
Structural Control of 1A2u-to-3A2u Intersystem Crossing in Diplatinum(II,II) Complexes (2012)

Analysis of variable-temperature fluorescence quantum yield and lifetime data for per(difluoroboro)tetrakis(pyrophosphito)diplatinate(II) ([Pt(2)(μ-P(2)O(5)(BF(2))(2))(4)](4-), abbreviated Pt(pop-BF(2))), yields a radiative decay rate (k(r) = 1.7 × 10(8) s(-1)) an order of magnitude greater than that of the parent complex, Pt(pop). Its temperature-independent and activated intersystem crossing (ISC) pathways are at least 18 and 142 times slower than those of Pt(pop) [ISC activation energies: 2230 cm(-1) for Pt(pop-BF(2)); 1190 cm(-1) for Pt(pop)]. The slowdown in the temperature-independent ISC channel is attributed to two factors: (1) reduced spin-orbit coupling between the (1)A(2u) state and the mediating triplet(s), owing to increases of LMCT energies relative to the excited singlet; and (2) diminished access to solvent, which for Pt(pop) facilitates dissipation of the excess energy into solvent vibrational modes. The dramatic increase in E(a) is attributed to increased P-O-P framework rigidity, which impedes symmetry-lowering distortions, in particular asymmetric vibrations in the Pt(2)(P-O-P)(4) core that would allow direct (1)A(2u)-(3)A(2u) spin-orbit coupling.
GELATINASE-A/MMP-2 SERUM LEVELS AND NEOPLASTIC PROGRESSION IN BREAST-CANCER PATIENTS (1994)

The metastatic potential of cancer cells has been associated to their ability to elaborate and secrete basement membrane degradative enzymes. In this process a major role appears to be played by a protease known as gelatinase A (72 kDa type IV collagenase, MMP-2). In an effort to assess the significance of these findings to breast cancer progression, we have evaluated the gelatinase A/MMP-2 serum levels in a cohort of 80 breast cancer patients, 27 subjects affected by benign breast disease and 27 healthy controls. Although differences between the three groups were observed, with the highest values monitored in benign breast disease, they were not statistically significant. On the contrary, within the breast cancer cohort, the patients presenting clinical evidence of distant metastases (M+, n=40) had statistically elevated enzyme serum levels (p<0.03) compared to those without nodal involvement and distant metastases (N-M-, n=20). The statistical significance was still evident when considering the overall M- cohort (including N+ and N- patients, n=40) compared to the M+. Although indicating that, in general, gelatinase A/MMP-2 is not a useful serum marker for breast cancer screening and diagnosis, the findings point toward its involvement in the breast cancer metastatic process and suggest a possible value in monitoring the outcome of the disease.