gebhart/patrepeval huggingface dataset:
Capture, isolation and release of cancer cells with aptamer-functionalized glass bead array (2012)

Early detection and isolation of circulating tumor cells (CTC) can enable better prognosis for cancer patients. A Hele-Shaw device with aptamer functionalized glass beads is designed, modeled, and fabricated to efficiently isolate cancer cells from a cellular mixture. The glass beads are functionalized with anti-epidermal growth factor receptor (EGFR) aptamer and sit in ordered array of pits in polydimethylsiloxane (PDMS) channel. A PDMS encapsulation is then used to cover the channel and to flow through cell solution. The beads capture cancer cells from flowing solution depicting high selectivity. The cell-bound glass beads are then re-suspended from the device surface followed by the release of 92% cells from glass beads using combination of soft shaking and anti-sense RNA. This approach ensures that the cells remain in native state and undisturbed during capture, isolation and elution for post-analysis. The use of highly selective anti-EGFR aptamer with the glass beads in an array and subsequent release of cells with antisense molecules provide multiple levels of binding and release opportunities that can help in defining new classes of CTC enumeration devices.
Development of high resolution Michelson interferometer for stable phase-locked ultrashort pulse pair generation (2008)

We developed a high resolution Michelson interferometer with a two-frequency He-Ne laser positioning system in order to stabilize the relative phase of a pulse pair. The control resolution corresponded to a 12 as time resolution or a phase of 1.5 degrees at 900 nm. This high resolution Michelson interferometer can generate a phase-locked pulse pair either with a specific relative phase such as 0 or pi radians or with an arbitrary phase. Coherent control of an InAs self-assembled quantum dot was demonstrated using the high resolution Michelson interferometer with a microspectroscopy system.
The IDOze Study: The Link Between Sleep Disruption and Tryptophan-Kynurenine Pathway Activation in Women With Human Immunodeficiency Virus (2022)

Abstract Background Poor sleep is associated with human immunodeficiency virus (HIV), particularly among women with HIV (WWH), although mechanisms are unclear. We explored cross-sectional associations between sleep disruption and tryptophan-kynurenine (T/K) pathway activation, measured by the kynurenine-to-tryptophan ratio (K:T). Methods HIV-uninfected women (HIV–) and WWH aged 35–70 years and on stable antiretroviral therapy were included. Sleep metrics were measured using wrist actigraphy. Plasma T/K pathway metabolites were measured using liquid chromatography–tandem mass spectrometry. Multivariate linear regression models examined relationships between K:T and actigraphy-based sleep metrics by HIV status. Results WWH (n = 153) and HIV– women (n = 151) were demographically similar. Among WWH, median CD4 was 751 cells/µL; 92% had undetectable HIV RNA. Compared to HIV– women, WWH had higher K:T (P &amp;lt; .001) and kynurenine (P = .01) levels but similar tryptophan levels (P = .25). Higher K:T was associated with more wake bouts (P = .001), more time awake after sleep onset (P = .01), and lower sleep efficiency (P = .03) in WWH only. Conclusions HIV infection was associated with T/K pathway activation; this activation was associated with poorer sleep efficiency and more fragmented sleep. While longitudinal studies are needed to elucidate the directionality of these associations, these findings may help identify treatments to reduce sleep disruption in WWH by targeting residual inflammation and T/K pathway activation.
Surface chemistry and beam-solid interactions (1991)

Although the symposium addressed a broad array of issues, some important common themes emerged. As an example, in the transition form thermally to non-thermally stimulated surface desorption processes, including laser ablation for thin film synthesis. Advanced diagnostic technique have made possible key experiments which indicate that the particle energy distributions and ionized fractions produced by laser ablation are in some instances very similar to those employed in low energy ion beam-assisted deposition processes. Another example, in the area of ion-solid interactions, was the similarities found between high energy and low energy beam-induced processes, such as damage and ion mixing. Overall, the symposium underscored the increasingly interdisciplinary nature of the field of beam-solid interactions. As the interests of chemists, physicists and materials scientist begin to converge in analysis of surface-related phenomena induced by beams whose energies range from a few to a few tens of eV, it is clear that many of the themes developed in this meeting will become active areas of future research.
Gain of a region on 7p22.3, containing <i>MAD1L1</i>, is the most frequent event in small‐cell lung cancer cell lines (2005)

Small-cell lung cancer (SCLC) is a highly aggressive lung neoplasm, which accounts for 20% of yearly lung cancer cases. The lack of knowledge of the progenitor cell type for SCLC precludes the definition of a normal gene expression profile and has hampered the identification of gene expression changes, while the low resolution of conventional genomic screens such as comparative genomic hybridization (CGH) and loss of heterozygosity analysis limit our ability to fine-map genetic alterations. The recent advent of whole genome tiling path array CGH enables profiling of segmental DNA copy number gains and losses at a resolution 100 times that of conventional methods. Here we report the analysis of 14 SCLC cell lines and six matched normal B-lymphocyte lines. We detected 7p22.3 copy number gain in 13 of the 14 SCLC lines and 0 of the 6 matched normal lines. In 4 of the 14 cell lines, this gain is present as a 350 kbp gene specific copy number gain centered at MAD1L1 (the human homologue of the yeast gene MAD1). Fluorescence in situ hybridization validated the array CGH finding. Intriguingly, MAD1L1 has been implicated to have tumor-suppressing functions. Our data suggest a more complex role for this gene, as MAD1L1 is the most frequent copy number gain in SCLC cell lines.
Outcome after Frontline Therapy with the Hyper-CVAD and Imatinib Mesylate Regimen for Adults with De Novo or Minimally Treated Philadelphia Chromosome (Ph) Positive Acute Lymphoblastic Leukemia (ALL) (2008)

Abstract Historically, complete remission (CR) rates with hyper-CVAD (cyclophosphamide, vincristine [VCR], doxorubicin and dexamethasone alternating with methotrexate and cytarabine) in de novo adult Ph-ALL were 90% or better; disease recurrence remained problematic. The selective ABL tyrosine kinase inhibitor (TKI) imatinib mesylate was thus incorporated into the hyper-CVAD regimen for de novo or minimally treated Ph-ALL [Thomas, Blood 103:4396, 2004]. The final regimen included imatinib 600 mg days 1–14 of induction, 600 mg continuously with courses 2–8, followed by escalation to 800 mg as tolerated during 24 mos of maintenance therapy with monthly VCR and prednisone interrupted by 2 intensifications with hyper-CVAD and imatinib, then imatinib indefinitely. Allogeneic stem cell transplant (SCT) was performed in first CR as feasible. The study accrued from April 2001 to September 2006. Fifty-four pts with imatinib-naive de novo or minimally treated Ph-ALL were treated. Forty-five pts had active disease, untreated (n=39) or refractory (n=6) to one induction course; 9 were in CR at start. Median age was 51 yrs (range, 17–84); 52% were male, and 13% had CNS disease at presentation. Of the 45 pts with active disease, 42 (93%) achieved CR (1 CRp, 1 partial response, 1 early death from sepsis). All 6 refractory patients achieved CR. Molecular CR rate (MCR, confirmed by nested PCR) prior to SCT was 52% overall. Sixteen pts (33%) underwent allogeneic SCT in first CR within a median of 5 mos from start of therapy (range 1–13). In the de novo group, 14 pts with median age of 37 yrs underwent allogeneic SCT in first CR whereas 33 pts with a median age of 53 years did not. The 3-yr survival (OS) rates were 66% vs 49% with or without SCT, respectively, p=0.36. The 3-yr CR duration rate was 84% for pts who achieved MCR (2 of 16 had SCT) compared to 64% for those who did not (14 of 35 had SCT), p=0.1; OS rates were similar regardless of MCR status. With a median follow-up of 52 mos (range 19–83+), 22% pts relapsed within a median of 15 mos from the start of therapy (range 8–42), including 2 after allogeneic SCT without imatinib maintenance. Detection of additional chromosome abnormalities at presentation did not influence outcome. In the de novo group, 4 of 9 evaluable relapses had ABL kinase domain mutations [E459K, Y253H, Y253F, F359V], none harbored T315I. The addition of imatinib improved outcome compared with hyper-CVAD alone (irrespective of allogeneic SCT); overall 3-yr CR duration and OS rates were 68% vs 25% and 55% vs 15%, respectively, p&amp;lt;0.001. Incorporation of second or later generation tyrosine kinase inhibitors into the hyper-CVAD regimen may further improve on the favorable imatinib experience. Allogeneic SCT in the TKI era needs to be reexamined in a prospective randomized trial.
A Novel Axially Chiral Phosphine-Oxazoline Ligand with an Axis-Unfixed Biphenyl Backbone: Preparation, Complexation, and Application in an Asymmetric Catalytic Reaction (2006)

A novel chiral phosphine-oxazoline ligand 3 with an axis-unfixed biphenyl backbone was prepared. This ligand existed as a mixture of two diastereomers in equilibrium in solution. However, when it was coordinated with palladium(II), only one of the two kinds of possible diastereomer complexes with different axial chirality was formed. When this axis-unfixed chiral ligand was used, up to 90% ee was attained for the palladium-catalyzed asymmetric allylic alkylation.
An algorithm for H/sub /spl infin// optimization of a linear time invariant system using singular value decomposition (1998)

Many classes of feedback control designs can be reformulated as a static output feedback optimization problem. Previous work by Burchett and Costello (1997) has exploited direct ways to compute the H/sub 2/ optimal output feedback gains using dyadic decomposition and analytic derivatives of the eigensystem. This work presents a modification of this technique with application to H/sub /spl infin// performance optimization. Analytic derivatives of the singular value decomposition (SVD) are central to this method. The method is applied to two aircraft flight control problems.
The current status of immunotoxins: an overview of experimental and clinical studies as presented at the Third International Symposium on Immunotoxins. (1993)

The Third International Symposium on Immunotoxins was held on June 19-21, 1992 in Orlando, Florida. This symposium was sponsored by NATO, NIH, Pierce Chemical Company, Walt Disney Cancer Institute at Florida Hospital, Duke Comprehensive Cancer Center, Xoma, Immunogen, Seragen, Bristol-Myers Squibb, Chiron, Ortho Biotech, Upjohn, Merck Sharp & Dohme Research Laboratories, Abbot Laboratories, Lilly Research Laboratories, and Evans & Sutherland. The Pierce Immunotoxin Award which recognizes outstanding contributions to immunotoxin research and development, was presented to Drs David FitzGerald, Fatih Uckun, David Eisenberg, and Ira Wool, for their contributions to the immunotoxin field.
Phase measurement system for meta-lens (2021)

In recent years, Meta-lens has become a new type of optical device, showing excellent performance and novel applications. The nanoantennas of meta-lens can be used to control the phase, amplitude, and polarization at well. The phase part is the most important part of the function of the meta-lens. However, so far, the phase distribution of meta-lenses has not been directly measured, which further hinders the quantitative evaluation of their performance. We have developed an interferometric imaging phase measurement system for meta-lens and meta-devices. This system can measure the phase distribution by shooting the interference pattern. The phase distribution of meta-lenses can be measured to quantitatively characterize the imaging performance. Our meta-lens phase measurement system can help for designers to optimize the design, for manufacturers to identify defects, thereby improving the manufacturing process. This work will pave the way for meta-lens in industrial applications.
Tetrahydrofuran Hydrate Crystal Growth Inhibitor Performance and Mechanism of Quaternary Ammonium and Phosphonium Salts (2020)

To gain insight into the hydrate crystal growth inhibitor (HCGIs) mechanism, we have studied various quaternary ammonium ionic liquid salts (QAILs) and phosphonium salts for their ability to prevent structure II (sII) hydrate crystal growth. We tested polyvinylpyrrolidone (PVP), polyvinylcaprolactam (PVCap), tetrapropylammonium bromide (TPrAB), tetrabutylammonium bromide (TBAB), tetrapentylammonium bromide (TPeAB), tetrahexylammonium bromide (THexAB), and tetrabutylphosphonium bromide (TBPB) in a tetrahydrofuran (THF) sII hydrate system using a unidirectional growth apparatus to determine the concentration and growth rate dependence. The growth rates of TPrAB, TBAB, and THexAB were found to be critical in the region of low growth rate, with the degree of supercooling ΔT becoming 0 for these additives in the low-growth-rate region. In contrast, PVP, PVCap, TPeAB, and TBPB remained effective at the lowest growth rate of V = 0.04 μm s–1. These trends can be explained by the residence time on the crystal surface of the HCGI, τ, and duration time of crystal growth.
Green Nanotechnology-based Gold Nanomaterials for Hepatic Cancer Therapeutics: A Systematic Review. (2020)

The objective of the current study was to systematically review the <i>in-vitro</i> anticancer activity of green synthesized gold nanoparticles (AuNPs) against hepatic cancer cells. The articles were identified through electronic databases, including PubMed, Scopus, Embase, Web of Science, Science Direct, ProQuest, and Cochrane. In total, 20 articles were found eligible to enter into our systematic review. Our findings showed that 65% of the articles used herbal extracts for the synthesis of AuNPs. Significantly, almost all of the articles stated the biofabrication of AuNPs below 100 nm in diameter. Impressively, most of the studies showed significant anticancer activity against HepG2 cells. Molecular studies stated the induction of apoptosis through the AuNPs-treated cells. We provided valuable information about the molecular mechanisms of AuNPs-induced cytotoxicity against HepG2 cells as well as their biocompatibility. The studies represented that AuNPs can be effective as anticancer drug nanocarrier for drug delivery systems. In addition, AuNP surface functionalization provides an opportunity to design multifunctional nanoparticles by conjugating them to diagnostic and/or therapeutic agents for theranostic purposes. Overall, our findings depicted considerable biogenic AuNPs-induced cytotoxicity, however, future studies should assess the anticancer activity of biogenic AuNPs through <i>in-vivo</i> studies, which was missing from such studies.
3D Vertebral Body Segmentation Using Shape Based Graph Cuts (2010)

Bone mineral density (BMD) measurements and fracture analysis of the spine bones are restricted to the Vertebral bodies (VBs). In this paper, we propose a novel 3D shape based method to segment VBs in clinical computed tomography (CT) images without any user intervention. The proposed method depends on both image appearance and shape information. 3D shape information is obtained from a set of training data sets. Then, we estimate the shape variations using a distance probabilistic model which approximates the marginal densities of the VB and background in the variability region. To segment a VB, the Matched filter is used to detect the VB region automatically. We align the detected volume with 3D shape prior in order to be used in distance probabilistic model. Then, the graph cuts method which integrates the linear combination of Gaussians (LCG), Markov Gibbs Random Field (MGRF), and distance probabilistic model obtained from 3D shape prior is used. Experiments on the data sets show that the proposed segmentation approach is more accurate than other known alternatives.
&lt;title&gt;Electric field dependence of optical properties of a double quantum well: experiment and applications&lt;/title&gt; (1990)

In the present work, we report the systematic observation of the optical blue shift induced by electric field in a GaAs/GaAIAs double-well system as far as 18 meV at room temperature. To this end, a detailed electroreflectance study of a GaAs-Alo.3 Gao.7 As double quantum well structure was carried out at room temperature. This effect occurs at moderate values ofthe applied field. In addition, a computer modeling of the electric field dependent optical properties is presented, which is based upon a variational calculation, in the frame of the effective mass approximation. The calculated spectra agree with the expefimental results. The model was used to engineer a coupled QW structure, which optimises the achievable modulation depth, due to application of an electric field.
Hepatocyte Growth Factor Activator Inhibitor Type 1 Is a Suppressor of Intestinal Tumorigenesis (2013)

Hepatocyte growth factor activator inhibitor type 1 (HAI-1/SPINT1) is a membrane-bound serine protease inhibitor expressed on the surface of epithelial cells. Although HAI-1/SPINT1 is abundantly expressed in the intestinal epithelium, its role in intestinal tumorigenesis is not known. In this study, we investigated the role of Hai-1/Spint1 in intestinal tumorigenesis using mouse models. The membranous Hai-1/Spint1 immunoreactivity was decreased in murine Apc(Min/+) tumors and also in carcinogen (azoxymethane treatment followed by dextran sodium sulfate administration)-induced colon tumors compared with the adjacent non-neoplastic epithelium. The decreased immunoreactivity appeared to be due to sheddase activity of membrane-type 1 matrix metalloprotease. Then, we examined the effect of intestine-specific deletion of Spint1 gene on Apc(Min/+) mice. The loss of Hai-1/Spint1 significantly accelerated tumor formation in Apc(Min/+) mice and shortened their survival periods. Activation of HGF was enhanced in Hai-1/Spint1-deficient Apc(Min/+) intestine. Gene expression profiling revealed upregulation of the Wnt/β-catenin signaling circuit, claudin-2 expression, and angiogenesis not only in tumor tissue but also in the background mucosa without macroscopic tumors in Hai-1/Spint1-deficient Apc(Min/+) intestine. Intestinal deletion of Spint1 also enhanced the susceptibility to carcinogen-induced colon tumorigenicity of wild-type Apc mice. Our findings suggest that HAI-1/SPINT1 has a crucial role in suppressing intestinal tumorigenesis, which implies a novel link between epithelial cell surface serine protease inhibitors and protection from carcinogenic stimuli.
Atomic Layer Deposition of Hafnium Oxide on InAs: Insight from Time-Resolved <i>in Situ</i> Studies (2020)

III-V semiconductors, such as InAs, with an ultrathin high-κ oxide layer have attracted a lot of interests in recent years as potential next-generation metal-oxide-semiconductor field-effect transistors, with increased speed and reduced power consumption. The deposition of the high-κ oxides is nowadays based on atomic layer deposition (ALD), which guarantees atomic precision and control over the dimensions. However, the chemistry and the reaction mechanism involved are still partially unknown. This study reports a detailed time-resolved analysis of the ALD of high-κ hafnium oxide (HfOx) on InAs(100). We use ambient pressure X-ray photoemission spectroscopy and monitor the surface chemistry during the first ALD half-cycle, i.e., during the deposition of the metalorganic precursor. The removal of In and As native oxides, the adsorption of the Hf-containing precursor molecule, and the formation of HfOx are investigated simultaneously and quantitatively. In particular, we find that the generally used ligand exchange model has to be extended to a two-step model to properly describe the first half-cycle in ALD, which is crucial for the whole process. The observed reactions lead to a complete removal of the native oxide and the formation of a full monolayer of HfOx already during the first ALD half-cycle, with an interface consisting of In-O bonds. We demonstrate that a sufficiently long duration of the first half-cycle is essential for obtaining a high-quality InAs/HfO2 interface.
First measurements on a novel type of optical micro-machined ultrasound transducer (OMUT) (2014)

Several types of ultrasound sensors have been developed and are used in the field of medical imaging. Conventional transducers are made of piezo-electric material and show good practical performance. However, when the piezo-electric elements need to be small (below 100 μm × 100 μm), these transducers face challenges in fabrication as well as the electrical impedance matching of the elements. As an alternative, we fabricated an optical micro-machined ultrasound transducer (OMUT). This sensor contains an optical micro-ring resonator, which is coupled to a photonic waveguide, and integrated onto an acoustical membrane. The OMUT is build with standard silicon-on-insulator (SOI) technology, allowing for easy fabrication. In this paper, we present the first measurement results of the sensor. Our prototype has a -6 dB bandwidth of 19% and a noise equivalent pressure (NEP) of 0.5 Pa. These first acoustical measurements show that this prototype may form the basis of future ultrasound transducers.
Mechanism of rat mesenteric arterial K<sub>ATP</sub> channel activation by 14,15-epoxyeicosatrienoic acid (2006)

Recently, we reported that 11,12-epoxyeicosatrienoic acid (11,12-EET) potently activates rat mesenteric arterial ATP-sensitive K(+) (K(ATP)) channels and produces significant vasodilation through protein kinase A-dependent mechanisms. In this study, we tried to further delineate the signaling steps involved in the activation of vascular K(ATP) channels by EETs. Whole cell patch-clamp recordings [0.1 mM ATP in the pipette, holding potential (HP) = 0 mV and testing potential (TP) = -100 mV] in freshly isolated rat mesenteric smooth muscle cells showed small glibenclamide-sensitive K(ATP) currents (19.0 +/- 7.9 pA, n = 5) that increased 6.9-fold on exposure to 5 microM 14,15-EET (132.0 +/- 29.0 pA, n = 7, P < 0.05 vs. control). With 1 mM ATP in the pipette solution, K(ATP) currents (HP = 0 mV and TP = -100 mV) were increased 3.5-fold on exposure to 1 microM 14,15-EET (57.5 +/- 14.3 pA, n = 9, P < 0.05 vs. baseline). In the presence of 100 nM iberiotoxin, 1 microM 14,15-EET hyperpolarized the membrane potential from -20.5 +/- 0.9 mV at baseline to -27.1 +/- 3.0 mV (n = 6 for both, P < 0.05 vs. baseline), and the EET effects were significantly reversed by 10 microM glibenclamide (-21.8 +/- 1.4 mV, n = 6, P < 0.05 vs. EET). Incubation with 5 microM 14,15-epoxyeicosa-5(Z)-enoic acid (14,15-EEZE), a 14,15-EET antagonist, abolished the 14,15-EET effects (31.0 +/- 11.8 pA, n = 5, P < 0.05 vs. 14,15-EET, P = not significant vs. control). The 14,15-EET effects were inhibited by inclusion of anti-G(s)alpha antibody (1:500 dilution) but not by control IgG in the pipette solution. The effects of 14,15-EET were mimicked by cholera toxin (100 ng/ml), an exogenous ADP-ribosyltransferase. Treatment with the ADP-ribosyltransferase inhibitors 3-aminobenzamide (1 mM) or m-iodobenzylguanidine (100 microM) abrogated the effects of 14,15-EET on K(ATP) currents. These results were corroborated by vasodilation studies. 14,15-EET dose-dependently dilated isolated small mesenteric arteries, and this was significantly attenuated by treatment with 14,15-EEZE or 3-aminobenzamide. These results suggest that 14,15-EET activates vascular K(ATP) channels through ADP-ribosylation of G(s)alpha.