gebhart/patrepeval huggingface dataset:
Laser induced fluorescence as a diagnostic tool integrated into a scanning fiber endoscope for mouse imaging (2007)

Scanning fiber endoscope (SFE) technology has shown promise as a minimally invasive optical imaging tool. To date, it is capable of capturing full-color 500-line images, at 15 Hz frame rate in vivo, as a 1.6 mm diameter endoscope. The SFE uses a singlemode optical fiber actuated at mechanical resonance to scan a light spot over tissue while backscattered or fluorescent light at each pixel is detected in time series using several multimode optical fibers. We are extending the capability of the SFE from a RGB reflectance imaging device to a diagnostic tool by imaging laser induced fluorescence (LIF) in tissue, allowing for correlation of endogenous fluorescence to tissue state. Design of the SFE for diagnostic imaging is guided by a comparison of single point spectra acquired from an inflammatory bowel disease (IBD) model to tissue histology evaluated by a pathologist. LIF spectra were acquired by illuminating tissue with a 405 nm light source and detecting intrinsic fluorescence with a multimode optical fiber. The IBD model used in this study was <i>mdr1a-/-</i> mice, where IBD was modulated by infection with <i>Helicobacter bilis</i>. IBD lesions in the mouse model ranged from mild to marked hyperplasia and dysplasia, from the distal colon to the cecum. A principle components analysis (PCA) was conducted on single point spectra of control and IBD tissue. PCA allowed for differentiation between healthy and dysplastic tissue, indicating that emission wavelengths from 620 - 650 nm were best able to differentiate diseased tissue and inflammation from normal healthy tissue.
Applied Nonlinear Dynamics and Stochastic Systems Near The Millenium. Proceedings (1997)

These proceedings represent papers presented at the Applied Nonlinear Dynamics and Stochastic Systems conference held in San Diego, California in July 1997. The conference emphasized the applications of nonlinear dynamical systems theory in fields as diverse as neuroscience and biomedical engineering, fluid dynamics, chaos control, nonlinear signal/image processing, stochastic resonance, devices and nonlinear dynamics in socio{minus}economic systems. There were 56 papers presented at the conference and 5 have been abstracted for the Energy Science and Technology database.(AIP)
Cerebral Brain Metabolism in Adult Dyslexic Subjects Assessed With Positron Emission Tomography During Performance of an Auditory Task (1992)

Ten dyslexic adults (aged 33.5 +/- 7.3 years, nine men, one woman) and 10 age-, sex- and handedness-matched control subjects (aged 33.6 +/- 5.8 years) performed an auditory syllable discrimination task during 18-fluoro-2-deoxyglucose uptake, and then underwent positron emission tomographic scans. A second normal control group performed an analogous visual discrimination task. Dyslexic subjects experienced greater difficulty and made significantly more errors in performing the auditory task. There were no differences in brain metabolic rates in lateral cortical areas (frontal, parietal, temporal, and occipital lobes). A significant difference emerged in the medial temporal lobe, with dyslexic subjects having significantly higher absolute and relative brain metabolism along an anterior-posterior gradient than normal adults. These data support the hypothesis of altered cerebral processing of auditory stimuli in patients with dyslexia.
Alpha 4 beta 7 integrin expression is associated with the leukemic evolution of human and murine T-cell lymphoblastic lymphomas. (1997)

We have previously shown that the in vivo coordinated expression of individual alpha 4 and beta 7 integrin chains correlated with the leukemic potential displayed by cell lines derived from murine lymphoblastic T-cell lymphomas (T-LBLs) when transplanted subcutaneously into syngeneic AKR mice. In the present study, by using immunofluorescence and immunocytochemical analyses, we have confirmed that the in vivo up-regulation of the alpha 4 beta 7 heterodimeric complex is associated with the leukemic behavior of AKR T-LBLs. In addition, when compared with the parental, highly leukemic NQ22 cells, the variant cell line NQ22V exhibited a reduced leukemic potential that was invariably associated with a delayed alpha 4 beta 7 up-regulation in vivo Moreover, the leukemic cell line SJ-1, derived from a spontaneous T-LBL of the SJL strain, also displayed high levels of alpha 4 beta 7 expression with a pattern of tissue distribution similar to that of NQ22 cells from leukemic AKR animals. Of note, in most of the tissues involved by murine T-LBL dissemination, and particularly in liver, kidney, and lung, alpha 4 beta 7-positive leukemic cells were always located around strongly VCAM-1-positive vascular spaces. These findings are consistent with a possible role of alpha 4 beta 7/VCAM-1 interactions in the extravasation and, consequently, in the leukemic dissemination of murine T-LBL cells. Immunocytochemical analysis carried out in 11 human T-LBLs showed that pathological lymph nodes from all 7 cases with bone marrow infiltration at presentation carried alpha 4 beta 7-positive cells, whereas all 4 aleukemic T-LBLs were repeatedly alpha 4 beta 7 negative, also in metachronous lesions. These findings suggest that alpha 4 beta 7-positive human T-LBLs may represent a distinct clinicopathological entity. In addition, alpha 4 beta 7 expression was significantly more prevalent in younger patients (< 11 years; P = 0.02), further supporting such a hypothesis. Moreover, as in murine T-LBLs, the pattern of alpha 4 beta 7 positivity in involved lymph nodes was mainly focal, whereas nearly all neoplastic cells infiltrating bone marrow expressed this integrin, suggesting a possible role for alpha 4 beta 7 in the leukemic dissemination also of human T-LBLs.
JNK inhibitor SP600125 promotes the formation of polymerized tubulin, leading to G2/M phase arrest, endoreduplication, and delayed apoptosis (2009)

The JNK inhibitor SP600125 strongly inhibits cell proliferation in many human cancer cells by blocking cell-cycle progression and inducing apoptosis. Despite extensive study, the mechanism by which SP600125 inhibits mitosis-related effects in human leukemia cells remains unclear. We investigated the effects of SP600125 on the inhibition of cell proliferation and the cell cycle, and on microtubule dynamics in vivo and in vitro. Treatment of synchronized leukemia cells with varying concentrations of SP600125 results in significant G2/M cell cycle arrest with elevated p21 levels, phosphorylation of histone H3 within 24 h, and endoreduplication with elevated Cdk2 protein levels after 48 h. SP600125 also induces significant abnormal microtubule dynamics in vivo. High concentrations of SP600125 (200 microM) were required to disorganize microtubule polymerization in vitro. Additionally, SP600125- induced delayed apoptosis and cell death was accompanied by significant poly ADP-ribose polymerase (PARP) cleavage and caspase-3 activity in the late phase (at 72 h). Endoreduplication showed a greater increase in ectopic Bcl-2-expressing U937 cells at 72 h than in wild-type U937 cells without delayed apoptosis. These results indicate that Bcl-2 suppresses apoptosis and SP600125-induced G2/M arrest and endoreduplication. Therefore, we suggest that SP600125 induces mitotic arrest by inducing abnormal spindle microtubule dynamics.
Simulation of flow‐flexible body interactions with large deformation (2011)

SUMMARY A modified front‐tracking method was proposed for the simulation of fluid‐flexible body interactions with large deformations. A large deformable body was modeled by restructuring the body using a grid adaptation. Discontinuities in the viscosity at the fluid‐structure interface were incorporated by distributing the viscosity across the interface using an indicator function. A viscosity gradient field was created near the interface, and a smooth transition occurred between the structure and the fluid. The fluid motion was defined on the Eulerian domain and was solved using the fractional step method on a staggered Cartesian grid system. The solid motion was described by Lagrangian variables and was solved by the finite element method on an unstructured triangular mesh. The fluid motion and the structure motion were independently solved, and their interaction force was calculated using a feedback law. The interaction force was the restoring force of a stiff spring with damping, and spread from the Lagrangian coordinates to the Eulerian grid by a smoothed approximation of the Dirac delta function. In the numerical simulations, we validated the effect of the grid adaptation on the solid solver using a vibrating circular ring. The effects of the viscosity gradient field were verified by solving the deformation of a circular disk in a linear shear flow, including an elastic ring moving through a channel with constriction, deformation of a suspended catenary, and a swimming jellyfish. A comparison of the numerical results with the theoretical solutions was presented. Copyright © 2011 John Wiley &amp; Sons, Ltd.
A novel viscous dissecting gel for endoscopic submucosal dissection: a prospective survival study in a porcine model (2014)

Hybrid ESD of large gastric lesions in a porcine model can be facilitated by the novel gel, dramatically reducing procedure and resection times by eliminating the need for time-consuming submucosal dissection. The novel gel is safe and easy to use, and has the potential to simplify ESD. Further prospective human studies are needed to validate these findings.
Ozone-Based Decomposition of Main Endocrine Disruption Chemicals in Sewage Effluent (2005)

In order to decompose endocrine disruption chemicals (EDCs) in sewage effluent, ozone based oxidation of nonylphenol (NP), bisphenol A (BPA) and 17β-estradiol (E2) was investigated. Experimental results showed that these EDCs were decomposed easily even in the presence of other organic substances of TOC 5 mg/L. The simulation using kinetic constants obtained from the experiments indicated that these EDCs in sewage effluent were removed to below the detection limit with an amount of ozone consumed less than 0.5 mg/L. Ozonation also reduced the estrogenic activity and the aquatic acute toxicity of these EDCs solution. From these results it was concluded that ozonation was very effective in decomposing these EDCs in sewage effluent.
Synthesis and Screening of a Random Dimeric Peptide Library Using the One-Bead−One-Dimer Combinatorial Approach (2006)

Large combinatorial libraries of random peptides have been used for a variety of applications that include analysis of protein-protein interactions, epitope mapping, and drug targeting. The major obstacle in screening these libraries is the loss of specific but low affinity binding peptides during washing steps. Loss of these specific binders often results in isolation of peptides that bind nonspecifically to components used in the selection process. Previously, it has been demonstrated that dimerizing or multimerizing a peptide can remarkably improve its binding kinetics by 10- to 1000-fold due to an avidity effect. To take advantage of this observation, we constructed a random library of 12 amino acid dimeric peptides on polyethylene glycol acrylamide (PEGA) beads by modifying the 'one-bead-one-compound' approach. The chemical synthesis of 100,000 peptides as dimers can be problematic due to steric and aggregation effects and the presence of many peptide sequences that are difficult to synthesize. We have designed a method, described in detail here, to minimize the problems inherent in the synthesis of a dimeric library by modifying the existing 'split and pool' synthetic method. Using this approach the dimeric library was used to isolate a series of peptides that bound selectively to epithelial cancer cells. One peptide with the amino acid sequence QMARIPKRLARH bound as a dimer to prostate cancer cells spiked into the blood but did not bind to circulating hematopoeitic cells. The monomeric form of this peptide, however, did not bind well to the same LNCaP cell line. These data demonstrate that "hits" obtained from such a 'one-bead-one-dimer' library can be used directly for the final application or used as leads for construction of second generation libraries.
Use of gene-editing technology to introduce targeted modifications in pigs (2018)

Pigs are an important resource in agriculture and serve as a model for human diseases. Due to their physiological and anatomical similarities with humans, pigs can recapitulate symptoms of human diseases, making them a useful model in biomedicine. However, in the past pig models have not been widely used partially because of the difficulty in genetic modification. The lack of true embryonic stem cells in pigs forced researchers to utilize genetic modification in somatic cells and somatic cell nuclear transfer (SCNT) to generate genetically engineered (GE) pigs carrying site-specific modifications. Although possible, this approach is extremely inefficient and GE pigs born through this method often presented developmental defects associated with the cloning process. Advancement in the gene-editing systems such as Zinc-Finger Nucleases (ZFNs), Transcription activator-like effector nucleases (TALENs), and the Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) system have dramatically increased the efficiency of producing GE pigs. These gene-editing systems, specifically engineered endonucleases, are based on inducing double-stranded breaks (DSBs) at a specific location, and then site-specific modifications can be introduced through one of the two DNA repair pathways: non-homologous end joining (NHEJ) or homology direct repair (HDR). Random insertions or deletions (indels) can be introduced through NHEJ and specific nucleotide sequences can be introduced through HDR, if donor DNA is provided. Use of these engineered endonucleases provides a higher success in genetic modifications, multiallelic modification of the genome, and an opportunity to introduce site-specific modifications during embryogenesis, thus bypassing the need of SCNT in GE pig production. This review will provide a historical prospective of GE pig production and examples of how the gene-editing system, led by engineered endonucleases, have improved GE pig production. We will also present some of our current progress related to the optimal use of CRISPR/Cas9 system during embryogenesis.
Validation of the COVAS (Comorbidities, Obesity, Vitals, Age, Sex) Score as a Practical Tool for Assessing Need for Intensive Care Services in Suspected SARS-CoV2 Patients (2020)

Background and Hypothesis Various scoring instruments have been proposed to risk-stratify patients with suspected COVID-19. Here we test prognostic system derived and tested in the Kaiser Permanente health system (the COVAS score). Experimental Design and Methods This was a primary analysis of the multicenter RECOVER registry, which includes patients tested for SARs-CoV-2 from 40 emergency departments around the US. We extracted components of COVAS score with two modifications, and computed a modified COVAS score, and used that as the “test” to compute the area under the receiver operating characteristic curve (AUROC) to predict any initial intensive care unit (ICU) admission or transfer to ICU. Results For SARS-CoV-2 positive patients, for the prediction of ICU admission, the COVAS AUROC=0.74 (95% CI = 0.72 to 0.77), with overall mean = 7.4 (SD=4.7), and the mean for ICU admission was higher (10.1, SD=4.6) versus no ICU admission (6.8, SD=4.5), p&lt;0.001 paired t-test. For SARS-CoV-2 negative patients, the COVAS score showed an AUROC= 0.70 (0.68-0.72) and the mean was 7.3, SD=4.2. Potential Impact The modified COVAS scoring system had modest overall discriminative value at predicting ICU admission, but was more accurate in SARS-CoV-2 positive patients, compared with SARs-CoV-2 negative suggesting the instrument is calibrated to predict ICU requirements in patients with suspected COVID-19, as opposed to functioning as a generic risk-stratification tool.
Characterizing various monoclonal antibodies with milder reversed phase chromatography conditions (2018)

Reversed phase liquid chromatography (RPLC) of therapeutic monoclonal antibodies (mAbs) is often performed at elevated temperatures (80–90 °C) and in the presence of relatively high concentrations of TFA (0.1%). Under such conditions, it is possible to achieve suitable performance in terms of peak shapes and recoveries. Yet, it is also possible, to cause on-column hydrolysis and the generation of artefact peaks. Interestingly, a wide-pore silica-based superficially porous (SPP) material with a high coverage phenyl bonding was recently introduced, and may offer a chance to perform protein RPLC with milder conditions (lower temperatures and lower TFA concentrations). To evaluate this possibility, 23 mAbs approved by Food and Drug Administration (FDA) and European Medicines Agency (EMA) were analysed on this new column, as well as a reference C4 SPP widepore silica-based column. Separations were performed at various temperatures ranging from 60 to 90 °C using various proportions of TFA and FA ranging from 0.1% TFA to 0.01% TFA/0.09% FA. It appears that temperature can be reduced down to 75 °C for intact mAbs and 65 °C for mAb subunits, using the high coverage phenyl bonded stationary phase. At such temperatures, desirable peak shape and&gt;90% recovery can be observed for each of the studied mAbs. To achieve the same performance with the reference C4 bonded stationary phase, it was necessary to work at 90 °C and 85 °C, respectively. In addition, for mAb subunit analysis, it has been found that combining the phenyl bonded stationary phase with a 0.03% TFA/0.07% FA mobile phase can yield separations similar those obtained with 0.1% TFA, but with an increase of mass spectrometric sensitivity by about 40%. This work provides examples of milder conditions (65 °C and 0.03% TFA+0.07% FA) being successfully employed in the RPLC(-MS) analysis of mAb subunits. A suitable stationary phase was selected, and milder conditions allow an improved MS sensitivity, while maintaining comparable elution profiles. Moreover, the use of milder conditions may reduce the risk of artefact peaks.
ChemInform Abstract: α‐Azidonation of Amides, Carbamates, and Ureas with the Iodosylbenzene/Trimethylsilyl Azide Reagent Combination: N‐Acyliminium Ion Precursors. (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.
An Exploratory Pathways Analysis of Temporal Changes Induced by Spinal Cord Injury in the Rat Bladder Wall: Insights on Remodeling and Inflammation (2009)

Our findings suggest that tissue remodeling, infection, inflammation, and tissue damage/dysfunction all play a role in the urinary bladder, in the complex response to SCI.
Nanostructures Boost the Thermoelectric Performance of PbS (2011)

In situ nanostructuring in bulk thermoelectric materials through thermo-dynamic phase segregation has established itself as an effective paradigm for optimizing the performance of thermoelectric materials. In bulk PbTe small compositional variations create coherent and semicoherent nanometer sized precipitates embedded in a PbTe matrix, where they can impede phonon propagation at little or no expense to the electronic properties. In this paper the nanostructuring paradigm is for the first time extended to a bulk PbS based system, which despite obvious advantages of price and abundancy, so far has been largely disregarded in thermoelectric research due to inferior room temperature thermoelectric properties relative to the pristine fellow chalcogenides, PbSe and PbTe. Herein we report on the synthesis, microstructural morphology and thermoelectric properties of two phase (PbS)(1-x)(PbTe)(x)x = 0-0.16 samples. We have found that the addition of only a few percent PbTe to PbS results in a highly nanostructured material, where PbTe precipitates are coherently and semicoherently embedded in a PbS matrix. The present (PbS)(1-x)(PbTe)(x) nanostructured samples show substantial decreases in lattice thermal conductivity relative to pristine PbS, while the electronic properties are left largely unaltered. This in turn leads to a marked increase in the thermoelectric figure of merit. This study underlines the efficiency of the nanostructuring approach and strongly supports its generality and applicability to other material systems. We demonstrate that these PbS-based materials, which are made primarily from abundant Pb and S, outperform optimally n-type doped pristine PbTe above 770 K.
Photoluminescence of nitrogen (N)-implanted and N-free In0.30Ga0.70P grown by liquid phase epitaxy (1980)

Photoluminescence (PL) studies were performed at 2 K for nitrogen (N)-implanted and N-free In0.30Ga0.70P crystals, which were grown by a step-cooling liquid-phase-epitaxial method. For the N-implanted In0.30Ga0.70P, an isoelectronic trap was found to be formed at annealing temperature over 600 °C. The binding energy of the excitons bound to the above traps was determined to be 92 meV from the temperature dependence of the PL spectra.
Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor (2020)

The proportion of fusobacteria in guts of southern Chinese populations are higher compared with several western and rural populations in line with the notion of environment/biogeography driving human gut microbiome composition. Several non-nucleatum taxa possess FadA homologues and were enriched in CRC cohorts; whether this imposes a risk in developing CRC and other gut diseases deserves further investigation.
Application specific data replication for edge services (2003)

The emerging edge services architecture promises to improve the availability and performance of web services by replicating servers at geographically distributed sites. A key challenge in such systems is data replication and consistency so that edge server code can manipulate shared data without incurring the availability and performance penalties that would be incurred by accessing a traditional centralized database. This paper explores using a distributed object architecture to build an edge service system for an e-commerce application, an online bookstore represented by the TPC-W benchmark. We take advantage of application specific semantics to design distributed objects to manage a specific subset of shared information using simple and effective consistency models. Our experimental results show that by slightly relaxing consistency within individual distributed objects, we can build an edge service system that is highly available and efficient. For example, in one experiment we find that our object-based edge server system provides a factor of five improvement in response time over a traditional centralized cluster architecture and a factor of nine improvement over an edge service system that distributes code but retains a centralized database.