gebhart/patrepeval huggingface dataset:
Nanoparticle Sizing and Potential Quality Control of Sols Using a Unique Fluorescence Anisotropy Probe and 3D Contour Anisotropy Mapping (2015)

Spectroscopic properties of the particle sizing fluorophore Dipole Blue are reported. The probe is cationic in nature, highly water-soluble, and strongly adheres to anionic silica surfaces by electrostatic interactions, as is demonstrated here by Ludox SM 30. The probe has a distinct absorbance band centered at 320 nm, and the fluorescence emission band is Stokes-shifted 100 nm with a peak centered at 426 nm. From time-correlated single-photon counting experiments, the fluorescence lifetime was found to be adequately described by a three-exponential decay model with an intensity-averaged lifetime of 15.6 ns. Perrin graph analysis of steady-state anisotropy shows the presence of silica particles with a radius of (5.44 ± 0.16) nm, which, considering the distribution of particle sizes, is in reasonable agreement with 3.5 nm found from dynamic light scattering experiments.
Coagulation factor XIII-A and activated FXIII-A decrease in some deep vein thrombosis patients following catheter-directed thrombolysis (2019)

: The objective of the study was to assess the effect of tissue plasminogen activator administered during catheter-directed thrombolysis (CDT) on coagulation factor XIII (FXIII). Thrombolytic therapy carries significant risks, such as life-threatening bleeds. The mechanisms responsible for major bleeds and intracerebral hemorrhages during thrombolysis are not fully understood. Activated FXIII (FXIII-A) lies at the intersection of coagulation and fibrinolysis. Using purified proteins and blood collected from nine deep vein thrombosis patients undergoing CDT, the stability of FXIII-A and FXIII were measured immediately before, immediately after and 1-day post thrombolysis. We found that purified tissue plasminogen activator directly degraded FXIII-A. During CDT, FXIII levels were decreased by more than 40% in five of nine patients and FXIII-A levels were decreased by more than 85% in two patients when it was activated. FXIII-A and FXIII-A can decrease during CDT in some patients, warranting further research into the role of FXIII-A in bleeding from thrombolysis.
Modellus (2012)

The rising complexity of distributed server applications in Internet data centers has made the tasks of modeling and analyzing their behavior increasingly difficult. This article presents Modellus , a novel system for automated modeling of complex web-based data center applications using methods from queuing theory, data mining, and machine learning. Modellus uses queuing theory and statistical methods to automatically derive models to predict the resource usage of an application and the workload it triggers; these models can be composed to capture multiple dependencies between interacting applications. Model accuracy is maintained by fast, distributed testing, automated relearning of models when they change, and methods to bound prediction errors in composite models. We have implemented a prototype of Modellus, deployed it on a data center testbed, and evaluated its efficacy for modeling and analysis of several distributed multitier web applications. Our results show that this feature-based modeling technique is able to make predictions across several data center tiers, and maintain predictive accuracy (typically 95% or better) in the face of significant shifts in workload composition; we also demonstrate practical applications of the Modellus system to prediction and provisioning of real-world data center applications.
Predictive performance of selected breath volatile organic carbon compounds in stage 1 lung cancer (2022)

Concentration of Acetoin in exhaled breath has low discrimination performance for S1LC cases and controls, while there was not enough evidence for twelve additional published VOCs.
Diffusion coded photography for extended depth of field (2010)

In recent years, several cameras have been introduced which extend depth of field (DOF) by producing a depth-invariant point spread function (PSF). These cameras extend DOF by deblurring a captured image with a single spatially-invariant PSF. For these cameras, the quality of recovered images depends both on the magnitude of the PSF spectrum (MTF) of the camera, and the similarity between PSFs at different depths. While researchers have compared the MTFs of different extended DOF cameras, relatively little attention has been paid to evaluating their depth invariances. In this paper, we compare the depth invariance of several cameras, and introduce a new camera that improves in this regard over existing designs, while still maintaining a good MTF. Our technique utilizes a novel optical element placed in the pupil plane of an imaging system. Whereas previous approaches use optical elements characterized by their amplitude or phase profile, our approach utilizes one whose behavior is characterized by its scattering properties. Such an element is commonly referred to as an optical diffuser, and thus we refer to our new approach as diffusion coding . We show that diffusion coding can be analyzed in a simple and intuitive way by modeling the effect of a diffuser as a kernel in light field space. We provide detailed analysis of diffusion coded cameras and show results from an implementation using a custom designed diffuser.
Highly selective etch gas chemistry design for precise DSAL dry development process (2014)

Dry development process for directed-self assembly lithography (DSAL) hole shrink process has been studied with focus on etch selectivity of poly(methyl methacrylate) (PMMA) to polystyrene (PS) and suppression of etch stop. Highly selective etch of PMMA to PS was achieved using CO gas chemistry. However, it was found that PMMA etching stopped proceeding beyond a certain depth. Scanning Transmission Electron Microscopy (STEM) and X-ray Photoelectron Spectroscopy (XPS) analysis indicated that a deposition layer formed not only on PS but also on PMMA. H<sub>2</sub> addition to CO plasma proved effective in controlling the deposition layer thickness and suppressing etch stop. CO/H<sub>2</sub> plasma process combined with ion energy control was applied to the dry development process for hole shrink. DSAL dry development process for hole shrink process was successfully realized by designing the etch gas chemistry and controlling ion energy.
Studies of a novel modified E2F-targeted peptide with activity against castration-resistant prostate cancer. (2017)

205 Background: The E2F family of genes encodes transcription factors that are key to the regulation of a number of target genes, including those encoding cyclins , CDKs , checkpoints regulators, and DNA repair and replication proteins. One of the primary functions of the E2Fs is to control the cell cycle, playing a major role in regulating the G1/S transition. One of the primary regulators of E2F expression is the retinoblastoma gene, RB, a chromatin associated protein that, in its unphosphorylated state, binds to and negatively regulates E2F; hyperphosphorylation of RB releases E2F, allowing cell cycle progression. Many tumor cells have mutant or dysfunctional RB, allowing the aberrant overexpression of the E2Fs and tumor cell proliferation; this aberrant overexpression is better tolerated when p53 is mutated, suppressing subsequent apoptosis. Overexpression of E2F, particularly E2F1, has thus been an attractive target for therapeutic intervention. However, this approach has not yet been successful, most likely due to the redundancy of the E2Fs and the lack of biomarkers for sensitivity. Methods: Using phage display, we have previously identified a novel peptide that, when coupled with penetratin (PEP) to enhance uptake), targets the E2F consensus site in E2F1,2 and 3a, leading to the downregulation of the activating E2Fs and their downstream targets. We have recently enhanced the stability and potency of this peptide by substituting L-Arg within the peptide with D-Arg. Results: Castrate resistant prostate cancer (CRPC) cells, DU-145, lack functional RB, have mutant p53, and are more sensitive to the D-Arg PEP than LnCap or PC-3 cells, with functional RB. Xenograft studies in mice show that the PEP, when encapsulated in PEGylated liposomes (PL-D-Arg PEP) , regresses DU-145 tumors without toxicity. Current studies are examining the combination of the (PL-D-Arg PEP) with taxotere, cisplatin and irradiation in prostate cancer xenografts and organoids from patients. Conclusions: A peptide that inhibits transcription of the activating E2Fs has promise to treat CRPC.
Tumor necrosis factor alpha inhibits collagen gene transcription and collagen synthesis in cultured human fibroblasts. (1988)

The effects of recombinant human tumor necrosis factor alpha (TNF alpha) on collagen production and gene expression in cultured fibroblasts were studied. Cells were labeled with [3H]proline, and the radioactivity of collagenase-sensitive and -resistant proteins were used to calculate the rates of protein production. The net production of collagen relative to total proteins was inhibited by TNF alpha (0-1.2 nM) in a dose- and time-related manner. The specific activities of the free [3H]proline pool, which were similar in control and TNF alpha-treated cells, were used to calculate the absolute rates of protein production. The absolute rate of collagen production was decreased by 50% in the presence of 1.2 nM TNF alpha during 24-h incubations (851 +/- 104 versus 426 +/- 39 pmol/micrograms of DNA/h; p less than 0.01), whereas noncollagen protein production and the rate of procollagen secretion were unchanged. We found no evidence of cellular toxicity in cultured cells treated with TNF alpha. In addition, TNF alpha did not affect cell proliferation as determined by [6-3H]thymidine incorporation into DNA. Most of the collagen produced by the cultured fibroblasts was type I. Using hybridization with specific DNA probes there was an approximately 50% decrease in the quantity of procollagen alpha 1(I) mRNA, without changes in the quantity of alpha tubulin mRNA or the size of the transcripts, in cells incubated with TNF alpha. Interleukin-1 (2.5 ng/ml) also decreased the levels of procollagen alpha 1(I) mRNA by approximately 50%. Cycloheximide (0.1 mM), an inhibitor of protein synthesis, blocked the inhibitory effect of both TNF alpha and interleukin-1 on procollagen alpha 1(I) mRNA. Nuclear run-off assays demonstrated that TNF alpha decreased procollagen alpha 1(I) transcriptional activity by 50% and had no effects on alpha tubulin gene transcription. Thus, TNF alpha decreases collagen gene transcription, collagen mRNA levels, and collagen production in cultured fibroblasts.
Thermal conductivity measurements of nitrogen-doped Ge<inf>2</inf>Sb<inf>2</inf>Te<inf>5</inf> (2011)

The thermal conductivity of nitrogen-doped Ge <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Sb <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Te <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sub> (N-GST) was analyzed using Frequency Domain Thermoreflectance (FDTR). The thermal conductivity of amorphous N-GST (~0.15 W/m-K) was not found to change significantly as the nitrogen concentration was raised from 0 at% to ~6 at%, possibly due to the huge amount of phonon scattering in the disordered films. The thermal conductivity of crystalline N-GST films was found to increase initially with increasing N content, but then to decrease upon further N addition. X-ray diffraction spectra of N-GST films show increasing defect density that correlates with the decrease in thermal conductivity of the crystalline films at higher nitrogen content.
Systemic Antibiotic Therapy for Chronic Osteomyelitis in Adults (2011)

The standard recommendation for treating chronic osteomyelitis is 6 weeks of parenteral antibiotic therapy. However, oral antibiotics are available that achieve adequate levels in bone, and there are now more published studies of oral than parenteral antibiotic therapy for patients with chronic osteomyelitis. Oral and parenteral therapies achieve similar cure rates; however, oral therapy avoids risks associated with intravenous catheters and is generally less expensive, making it a reasonable choice for osteomyelitis caused by susceptible organisms. Addition of adjunctive rifampin to other antibiotics may improve cure rates. The optimal duration of therapy for chronic osteomyelitis remains uncertain. There is no evidence that antibiotic therapy for >4-6 weeks improves outcomes compared with shorter regimens. In view of concerns about encouraging antibiotic resistance to unnecessarily prolonged treatment, defining the optimal route and duration of antibiotic therapy and the role of surgical debridement in treating chronic osteomyelitis are important, unmet needs.
Cloning and characterization of bacteriophage-like DNA from Haemophilus somnus homologous to phages P2 and HP1 (1997)

In an attempt to identify and characterize components of a heme uptake system of Haemophilus somnus, an Escherichia coli cosmid library of H. somnus genomic DNA was screened for the ability to bind hemin (Hmb+). The Hmb+ phenotype was associated with a 7,814-bp HindIII fragment of H. somnus DNA that was subcloned and sequenced. Thirteen open reading frames (orfs) were identified, all transcribed in one direction, and transposon mutagenesis identified orf7 as the gene associated with the Hmb+ phenotype. Orf7 (178 amino acids) has extensive homology with the lysozymes of bacteriophages P-A2, P21, P22, PZA, phi-29, phi-vML3, T4, or HP1. The orf7 gene complemented the lytic function of the K gene of phage P2 and the R gene of phage lambda. A lysozyme assay using supernatants from whole-cell lysates of E. coli cultures harboring plasmid pRAP501 or pGCH2 (both of which express the orf7 gene product) exhibited significant levels of lysozyme activity. The orf6 gene upstream of orf7 has the dual start motif common to the holins encoded by lambdoid S genes, and the orf6 gene product has significant homology to the holins of phages HP1 and P21. When expressed from a tac promoter, the orf6 gene product caused immediate cell death without lysis, while cultures expressing the orf7 gene product grew at normal rates but lysed immediately after the addition of chloroform. Based on this data, we concluded that the Hmb+ phenotype was an artifact resulting from the expression of cloned lysis genes which were detrimental to the E. coli host. The DNA flanking the cloned lysis genes contains orfs that are similar to structural and DNA packaging genes of phage P2. Polyclonal antiserum against Orf2, which is homologous to the major capsid precursor protein (gpN) of phage P2, detected a 40,000-M(r) protein expressed from pRAP401 but did not detect Orf2 in H. somnus, lysates. The phage-like DNA was detected in the serum-susceptible preputial strains HS-124P and HS-127P but was absent from the serum-resistant preputial strains HS-20P and HS-22P. Elucidation of a potential role for this cryptic prophage in the H. somnus life cycle requires more study.
Abstract 2964: Immuno-reactive cancer organoid models to examine microbiome metabolite effects on immune checkpoint blockade efficacy (2021)

Abstract Introduction: As the number of available immunotherapies for solid tumors increase, their prevalence in the clinic continues to rise as well. While the results are promising, and immunotherapies have benefits over traditional chemotherapeutics, a sizable percentage of patients are non-responders to all types of immunotherapy. These differences in sensitivity can be either innate or acquired. Yet, there has been limited 3D in vitro models to assess tumor immune-reactivity. These systems are ideal for isolating specific molecular mechanisms that dictate cell behavior and interactions. Our goal was to create an organoid model containing cancer cells paired with cytotoxic T-cells to model immune checkpoint blockade (ICB) efficacy. This model could then be used to examine novel microbiome-ICB interactions shown by recent research to alter therapeutic response levels in patients. Methods: We created tumor organoids consisting of tumor and immune cells, embedded in extracellular matrix (ECM)-like hydrogels. Organoids were treated with therapeutic equivalent doses of anti-PD-1 and anti-CTLA-4 or single dose of anti-CD-47 and cell viability assays, flow cytometry, RT-qPCR, and immunohistochemistry staining were performed to determine the effects of ICB. Physiologic concentrations of metabolites derived from likely effector bacterial species were then evaluated for their effects on genetic expression and immunotherapy efficacy. Results and Discussion: We showed that ICB therapy stimulated internally localizing T-cells, inducing T-cell-mediated tumor cell killing. ICB treated samples resulted significant loss of viability with corroborating readings from the other methods of characterization. RT-qPCR resulted in some elucidation of potential cellular changes due to bacterial metabolites with further quantification ongoing. Conclusion: We have created an ex-vivo tumor immune-reactive organoid model for studying immunotherapy. We can now continue to change individual microenvironment factors, such as microbiome metabolites, and observe their impacts on immunotherapy efficacy to better understand what conditions are conducive or detrimental to successful ICB treatment. Citation Format: Ethan Shelkey, David Soto-Pantoja, Yong Lu, Shay Soker. Immuno-reactive cancer organoid models to examine microbiome metabolite effects on immune checkpoint blockade efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2964.
A fully integratable 1.55-μm wavelength continuously tunable asymmetric twin-waveguide distributed Bragg reflector laser (2003)

We demonstrate a single-frequency continuously tunable three-section distributed Bragg reflector laser operating at a center wavelength of /spl lambda/ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> =1.548 μm using a fully integratable asymmetric twin-waveguide structure. A low-loss tapered mode transformer couples the light between the active waveguide, or gain region, and the passive ridge waveguide where the phase and grating tuning sections are located. The device has a threshold current of 50 mA and output power of nearly 13 mW, with a slope efficiency of 0.12 W/A and a tuning range of 4.8 nm under pulsed operation. An independent phase section is used to continuously tune the wavelength, thus avoiding mode hops. Using a delayed self-heterodyne technique, we determine the linewidth to be (146/spl plusmn/2) kHz.
Velocity‐selective RF pulses in MRI (2005)

A family of velocity-selective pulses consisting of a series of RF hard pulses followed by bipolar gradients was designed. The succession of required pulses was deduced using a k-space approach within a small tip-angle approximation. Fourier transform of the desired velocity excitation determined the flip-angle series, and the corresponding position in the generalized k-space identified the bipolar-gradient first moments. Spins from any velocity class can be selected. To illustrate this approach we designed and experimentally tested a velocity-slice selection that is analogous to standard spatial-slice selection but involves excitation of spins moving at a chosen velocity (velocity-slice center) and within a given interval (velocity-slice thickness). The assumed approximation does not limit the design to small angles, because velocity selection still holds for angles up to 90 degrees. Velocity slices were experimentally selected, centered on velocities ranging from -1 m s(-1) to 1 m s(-1) with a velocity-slice thickness of 0.4 m s(-1). The experimental velocity-slice profile was assessed and the flow was quantified.
ChemInform Abstract: Enantioselective and Practical Syntheses of (R)‐ and (S)‐Fluoxetines. (1990)

Abstract Chloroethyl phenyl ketone (I) is stereoselectively reduced with borane in the presence of a chiral oxazolidine to give the chloro alcohol (II).
Primärdiagnostik und Verlaufskontrolle der akuten Lungenembolie: Vergleich zwischen digitaler Subtraktionsangiographie und Spiral-CT (1994)

The aim of this prospective study was to evaluate Spiral CT in the primary diagnosis of acute pulmonary emboli and for follow-up after thrombolytic treatment. Digital subtraction angiography of the lung was used as the reference method. 38 patients were subjected to both procedures. 79% of Spiral CT and 63% of DSA examinations were optimal. The two methods agreed in the diagnosis of thrombo-embolism in 30 patients and excluded it in eight patients. Spiral CT verified thrombi in a total of 213 cases; of these 23 were in a main pulmonary artery (11%), 88 in lobar arteries (41%), and 102 in segmental arteries (48%). DSA demonstrated 180 thrombi. 17% of the adherent and partially occlusive thrombi were not shown. 38 pulmonary infarcts were found in 18 patients. In 15 patients resolution of thrombi following thrombolytic treatment was shown by Spiral CT. Spiral CT is an excellent alternative to DSA and its use in the diagnosis of pulmonary emboli is entirely appropriate.
Outcome of refractory and relapsed acute myeloid leukemia in children treated during 2005-2011 – experience of the Polish Pediatric Leukemia/Lymphoma Study Group (PPLLSG) (2014)

The uniform reinduction regimen of the documented efficacy and subsequent alloHSCT in remission is needed to improve the outcome for ref/relAML children treated within PPLLSG. The focus should be on the future risk-directed both front and second line AML therapy.
A new method to decrease grating sidelobes level in medical acoustic arrays (2003)

The design of a medical acoustic array for a given echographic system is often a compromise between the lateral resolution and the grating sidelobe level. For a fixed number of active channels, the only way to decrease the grating sidelobe level is to decrease the array pitch. This can be done by working with an acoustical pitch smaller than the electrical pitch, which is possible by using an electrical passive interpolation circuit between the electrical channels and the transducers. This method takes advantage of the fact that in echographic systems the sampling of the array is generally limited by the maximum number of electronic channels and not by the minimum technically achievable pitch on the transducer. The theoretical analysis and design of such arrays are described. This technique was used to construct a 3.75-MHz curved array. The result is a 10-dB improvement of the sidelobe level.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Electrolyzer and method of use (2023)

Disclosed are membrane electrode assemblies having a cathode layer comprising a carbon oxide reduction catalyst that promotes reduction of a carbon oxide; an anode layer comprising a catalyst that promotes oxidation of a water; a polymer electrolyte membrane (PEM) layer disposed between, and in contact with, the cathode layer and the anode layer; and a salt having a concentration of at least about 10 uM in at least a portion of the MEA.