gebhart/patrepeval huggingface dataset:
Convenient Automated Conductance Volumetric System. (2002)

Conventional conductance volumetric systems require ex-vivo calibrations for blood conductivity and parallel conductance. It is often impractical to repeat blood sampling and hypertonic saline infusion for these calibrations. To overcome these limitations, we developed a useful, self-calibrating conductance volumetric system that does not require ex-vivo calibrations. On a conventional 6-electrode catheter, we added an extra electrode close to one of the recording electrodes to estimate blood conductivity. These two electrodes were placed close (0.5 mm) enough so that conductance between them reflected only blood conductivity regardless of cardiac volume. We estimated parallel conductance by the dual-frequency excitation (2 and 20 kHz) method. In 18 anesthetized rabbits, blood conductivity (sigma(est)) thus estimated agreed well with that (sigma(conv)) measured by the conventional ex-vivo blood sampling method (sigma(est) = 1.04sigma(conv)-0.25, R(2) = 0.98, SEE = 0.01 mS/cm, 1.2% error). Parallel conductance (G(p est)) estimated by dual-frequency excitation also agreed well with that (G(p conv)) estimated by the saline injection method (G(p est) = 0.95G(p conv)+4.25, R(2) = 0.87, SEE = 4.0 mS, 6.0% error). Estimated ventricular volume (V(est)) by our system agreed reasonably well with that (V(conv)) by the conventional method (V(est) = 0.93V(conv)+0.01, R(2) = 0.86, SEE = 0.22 ml, 14.7% error). The fact that this self-calibrating conductance volumetric system drastically simplifies volume measurement makes it an attractive tool for the assessment of cardiac function where significant changes in blood conductivity and parallel conductance are inevitable, such as in cardiac surgery.
Infection After Shoulder Instability Surgery (2003)

Currently, there are no reported series on the outcome of patients treated for infection after shoulder instability surgery. Therefore, the purpose of this study was to review patients who were treated for infection after shoulder instability surgery at our institution between 1980 and 2001 to determine the functional outcome and organisms responsible for infection. During this period, six patients were treated for infection after shoulder instability surgery. Three patients had an early postoperative infection, presenting 6 weeks or less from the time of instability surgery. Three patients had a late infection, presenting 8 months or greater from the time of surgery. Each of the three patients with a late infection had a sinus leading to a retained nonabsorbable suture. None of the six patients have had recurrent shoulder instability. Three patients had a polymicrobial infection and three patients had single organisms. Infection may be acute or significantly delayed from the time of the instability procedure. Additionally, among patients with late infection, there should be a high degree of suspicion for a nidus of infection surrounding nonabsorbable sutures.
Low-Power Circuit for Measuring and Compensating Phase Interpolator Non-Linearity (2019)

In this paper, we propose a novel circuit and technique to measure and pre-compensate for the differential and integral non-linearities (DNL and INL) of phase interpolators (PIs). The circuit can be used in Serializer/De-serializer (SerDes) and phase interpolator-based clock recovery circuity. The test circuit, implemented in 28 nm FD-SOI technology as part of optical transceiver, shows that the solution enabled a reduction in system total jitter.
Front Matter: Volume 6834 (2007)

This PDF file contains the front matter associated with SPIE Proceedings Volume 6834, including the Title Page, Copyright information, Table of Contents, Introduction, and the Conference Committee listing.
Role of Agglomeration in Calcium Oxalate Monohydrate Urolith Development (1992)

Formation of agglomerates of calcium oxalate monohydrate (COM) crystals on semi-batch precipitation performed at conditions relevant to urolithiasis (37 degrees C, pH = 6, initial ratio [Ca]/[Ox] = 10), but without any specific admixture, was followed by both optical and electron microscopy. COM crystals formed on precipitation developed into large agglomerates consisting of intergrown crystals by a mechanism of primary agglomeration. Primary agglomeration of COM crystals represents an important mechanism of COM renal calculi growth.
Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy (2006)

We report here the design, synthesis and application of pyrene binary oligonucleotide probes for selective detection of cellular mRNA. The detection strategy is based on the formation of a fluorescent excimer when two pyrene groups are brought into close proximity upon hybridization of the probes with the target mRNA. The pyrene excimer has a long fluorescence lifetime (>40 ns) compared with that of cellular extracts (approximately 7 ns), allowing selective detection of the excimer using time-resolved emission spectra (TRES). Optimized probes were used to target a specific region of sensorin mRNA yielding a strong excimer emission peak at 485 nm in the presence of the target and no excimer emission in the absence of the target in buffer solution. While direct fluorescence measurement of neuronal extracts showed a strong fluorescent background, obscuring the detection of the excimer signal, time-resolved emission measurements indicated that the emission decay of the cellular extracts is approximately 8 times faster than that of the pyrene excimer probes. Thus, using TRES of the pyrene probes, we are able to selectively detect mRNA in the presence of cellular extracts, demonstrating the potential for application of pyrene excimer probes for imaging mRNAs in cellular environments that have background fluorescence.
Optical Microstructures for High Performance Inertial Sensors (2019)

We report progress on precision optical microstructures such as a postage stamp-sized optics table aimed at miniaturization and cost reduction of navigation-grade gyroscopes. Other chip-scale developments include an optical waveguide-based laser gyroscope, and resonant opto-mechanical structures with optical readout for gun-hard gyroscopes and accelerometers, respectively.
Performance of Nomogram Prediction Combining MiRNAs in Cervical Mucus, HPV Genotype and Age for Cervical Cancer and its Precursor Lesions (2022)

Abstract Cervical cancer is the fourth most common cancer in women worldwide. Although cytology or HPV testing is available for screening, these techniques have their drawbacks and optimal screening methods are still being developed. Here, we sought to determine whether aberrant expression of miRNAs in cervical mucus could be an ancillary test for cervical neoplasms. The presence of miRNAs in 583 and 126 patients (validation and external cohorts) was determined by real-time RT-PCR. Performance of a combination with five miRNAs (miR-126-3p, -451a -144-3p, -20b-5p and -155-5p) was estimated by ROC curve analysis. Predicted probability (PP) was estimated by nomograms comprising -ΔCt values of the miRNAs, HPV genotype and age. A combination of five miRNAs showed a maximum AUC of 0.956 (95%CI: 0.933-0.980) for discriminating cancer. Low PP scores were associated with good prognosis over the 2-year observation period ( p &lt;0.05). Accuracy for identifying cancer and cervical intraepithelial neoplasia (CIN)3+ by nomogram was 0.983 and 0.966, respectively. PP was constant with different storage conditions of materials. We conclude that nomograms using miRNAs in mucus, HPV genotype and age could be useful as ancillary screening tests for cervical neoplasia.
MBIR 3D Reconstruction Method Effectively Minimizes Missing Wedge Artifacts and Restores Missing Information in Cryo-electron Tomography (2020)

Cryo-electron tomography (cryo-ET) has emerged as an essential technique that allows us to reveal macromolecular complexes and cellular architecture in their near-native states In cryo-ET, the biological samples are imaged as they are tilted at different projection angles around a tilt axis, resulting in 2D tilt series that can be reconstructed to 3D tomograms However, due to the radiation damage and the limited tilt range, cryo-ET suffers from low contrast and missing wedge artifacts, which deteriorates the resolution of 3D reconstruction and weakens the interpretability of the reconstructed tomogram To address these challenges, we introduced the Model-Based Iterative Reconstruction (MBIR) method
Cholesterol starvation induces differentiation of the intestinal parasite Giardia lamblia. (1996)

Giardia lamblia, like most human intestinal parasitic protozoa, sustains fundamental morphological and biochemical changes to survive outside the small intestine of its mammalian host by differentiating into an infective cyst. However, the stimulus that triggers this differentiation remains totally undefined. In this work, we demonstrate the induction of cyst formation in vitro when trophozoites are starved for cholesterol. Expression of cyst wall proteins was detected within encystation-specific secretory vesicles 90 min after the cells were placed in lipoprotein-deficient TYI-S-33 medium. Four cloned lines derived from two independent Giardia isolates were tested, and all formed cysts similarly. Addition of cholesterol, low density or very low density lipoproteins to the lipoprotein-deficient culture medium, inhibited the expression of cyst wall proteins, the generation of encystation-specific vesicles, and cyst wall biogenesis. In contrast, high density lipoproteins, phospholipids, bile salts, or fatty acids had little or no effect. These results indicate that cholesterol starvation is necessary and sufficient for the stimulation of Giardia encystation in vitro and, likely, in the intestine of mammalian hosts.
PRISMA extension for moxibustion 2020: recommendations, explanation, and elaboration (2020)

We have registered it on the EQUATOR (Enhancing the QUAlity and Transparency Of health Research) network, particularly under the item of PRISMA-TCM: http://www.equator-network.org/library/reporting-guidelines-under-development/reporting-guidelines-under-development-for-systematic-reviews/#65 .
Pan-phylum Comparison of Nematode Metabolic Potential (2015)

Nematodes are among the most important causative pathogens of neglected tropical diseases. The increased availability of genomic and transcriptomic data for many understudied nematode species provides a great opportunity to investigate different aspects of their biology. Increasingly, metabolic potential of pathogens is recognized as a critical determinant governing their development, growth and pathogenicity. Comparing metabolic potential among species with distinct trophic ecologies can provide insights on overall biology or molecular adaptations. Furthermore, ascertaining gene expression at pathway level can help in understanding metabolic dynamics over development. Comparison of biochemical pathways (or subpathways, i.e. pathway modules) among related species can also retrospectively indicate potential mistakes in gene-calling and functional annotation. We show with numerous illustrative case studies that comparisons at the level of pathway modules have the potential to uncover biological insights while remaining computationally tractable. Here, we reconstruct and compare metabolic modules found in the deduced proteomes of 13 nematodes and 10 non-nematode species (including hosts of the parasitic nematode species). We observed that the metabolic potential is, in general, concomitant with phylogenetic and/or ecological similarity. Varied metabolic strategies are required among the nematodes, with only 8 out of 51 pathway modules being completely conserved. Enzyme comparison based on topology of metabolic modules uncovered diversification between parasite and host that can potentially guide therapeutic intervention. Gene expression data from 4 nematode species were used to study metabolic dynamics over their life cycles. We report unexpected differential metabolism between immature and mature microfilariae of the human filarial parasite Brugia malayi. A set of genes potentially important for parasitism is also reported, based on an analysis of gene expression in C. elegans and the human hookworm Necator americanus. We illustrate how analyzing and comparing metabolism at the level of pathway modules can improve existing knowledge of nematode metabolic potential and can provide parasitism related insights. Our reconstruction and comparison of nematode metabolic pathways at a pan-phylum and inter-phylum level enabled determination of phylogenetic restrictions and differential expression of pathways. A visualization of our results is available at http://nematode.net and the program for identification of module completeness (modDFS) is freely available at SourceForge. The methods reported will help biologists to predict biochemical potential of any organism with available deduced proteome, to direct experiments and test hypotheses.
Localization of transected wire. (1991)

Localization of transected wire.J S Mitnick, M F Vazquez, M N Harris and S S BuchbinderAudio Available | Share
Laser-induced fluorescence spectroscopy at endoscopy: tissue optics, Monte Carlo modeling, and in vivo measurements (1995)

The optical properties (absorption coefficient, scattering coefficient and the anisotropic factor of scattering) and fluorescence characteristics of normal and abnormal bronchial tissue were measured in vitro. After adding additional blood optical properties to in vitro optical properties of tissue, the <i>in vivo</i> bronchial fluorescence was simulated and analyzed by Monte Carlo modeling. The Monte Carlo simulation results showed that with an appropriate illumination and fluorescence collection geometry, the distortion of <i>in vivo</i> fluorescence spectra of tissue caused by variations of optical properties at different wavelengths could be much reduced. Based on these results, a spectrofluorometry system was developed for the collection of <i>in vivo</i> laser-induced fluorescence spectra of tissue during endoscopy. In comparing the <i>in vivo</i> fluorescence spectral shape of bronchial tissue collected by this system with the intrinsic one obtained in vitro, we found no obvious distortion in the <i>in vivo</i> spectra. This was completely consistent with the analysis of Monte Carlo modeling. The <i>in vivo</i> measurement results demonstrated that significant differences in fluorescence intensity between normal and diseased bronchial tissue (dysplasia, carcinoma in situ) can be used to differentiate them from each other. Also, changes in fluorescence intensity are more robust for detecting abnormal tissues than the differences in spectral characteristics.
Space Requirements for Wheeled Mobility Devices in Public Transportation: Analysis of Clear Floor Space Requirements (2010)

Recent research on the anthropometry of wheeled mobility devices and their users (<i>n</i>=<i>369</i>) indicates that the current dimensions for 'clear floor area' prescribed in U.S. accessibility standards for transportation are inadequate for accommodating many users of wheeled mobility devices, especially those that use power chairs and scooters. The current report presents anthropometry data for determining the dimensions of clear floor area based on occupied device length and width to achieve a specified level of physical accommodation. The implications of the findings and the need for revising guidelines for accessible public transportation systems are discussed. It is important that the transportation industry as well as mobility device manufacturers, vendors and prescribers understand the limitations of current standards and becomes involved in the dialogue about how to address the need for improving them.
Therapeutic Control of Oral Anticoagulant Treatment in the Netherlands (1988)

Therapeutic control achieved by an anticoagulant clinic may be assessed by calculation of the proportion of time spent by the patients within the prothrombin time target range aimed for by the clinic. Three calculation methods for such assessment have been described by other investigators. The three methods were compared with the use of the database of one anticoagulant clinic (Leiden Thrombosis Centre). Discrepant levels of control were obtained by these methods because of incorrect assumptions in two of them. The most accurate method is the "cross-section-of-the-files" approach, in which the last-recorded prothrombin time per patient is used. The authors believe it should be implemented in each anticoagulant clinic. With the use of this method, the level of therapeutic control achieved by the Leiden Thrombosis Centre for its patients on long-term treatment amounted to 80%. The same method was applied by 37 other thrombosis centers in the Netherlands using a single target range of 2.8-4.8 International Normalized Ratio for their patients. Thirty-one centers achieved a level of control of at least 70% in their long-term patients. Underanticoagulation was observed more frequently than overanticoagulation.
ATIM-32. PERSONALIZED NEOANTIGEN-TARGETING VACCINE GENERATES ROBUST SYSTEMIC AND INTRATUMORAL T CELL RESPONSES IN GLIOBLASTOMA (GBM) PATIENTS (2018)

The impact of individualized neoepitope vaccination targeting neoantigens arising from tumor-specific mutations for GBM, a low mutation burden tumor with an immunologically cold tumor microenvironment, as well as that of concurrently administered dexamethasone (dex), are unknown. Individualized vaccination of up to 20 synthetic, long neoepitope peptides with high predicted HLA binding affinity admixed with poly-ICLC, were administered subcutaneously using a prime-boost schedule after RT to newly diagnosed, MGMT unmethylated, at least partially resected, GBM patients without progression after radiation (RT) in our phase 1b study. 9 of 10 screened patients had sufficient (10) identified neoepitope peptides. 8 patients without progression after RT received vaccine consisting of a median of 12 peptides (range, 7–20) beginning a median of 19.9 wks (range 17.1–24.7) after surgery. Adverse events were limited to infrequent grade 1/2 local reactions and fatigue. Median PFS and OS were 7.5 mths (90% CI: 6.2, 9.7) and 16.8 mths (90% CI: 9.6, 21.3). Evaluation of neoepitope-specific immune responses and tumor immune infiltrate analyses were performed on five patients with pre- and post-vaccination samples. Three patients on dex for post-RT edema during vaccine had no immune responses and no change in tumor infiltrating effector cells. In contrast 2 patients not on dex had robust, de novo immune responses against multiple predicted personal neoantigens including polyfunctional neoantigen-specific CD4+ and CD8+ T cell responses that were enriched for memory and activated phenotypes as well as increased numbers of tumor-infiltrating CD4+ and CD8+ T cells. T cell receptor analysis from one patient identified identical clonotypes isolated from post-vaccination tumor tissue and peripheral blood including two clonotypes specific for ARHGAP35, a neoantigen targeted by vaccination. Individualized, multi-neoepitope vaccines are feasible, safe and capable of generating systemic and intra-tumoral immune responses in GBM patients that appear to be abrogated by dex.
Oriented FAU Zeolite Films on Micrometer-Sized EMT Crystals (1999)

Permeability is a crucial aspect of zeolite films, and is a characteristic that is dependent on the orientation of the individual zeolite crystals that compose the film. In this communication is reported oriented zeolite films of FAU structure-type on compositionally different, micrometer-sized EMT zeolite crystals. The Figure depicts the edge of such a film, and shows that the FAU overgrowth is oriented and highly crystalline.
PAX6 Isoforms, along with Reprogramming Factors, Differentially Regulate the Induction of Cornea-specific Genes (2016)

PAX6 is the key transcription factor involved in eye development in humans, but the differential functions of the two PAX6 isoforms, isoform-a and isoform-b, are largely unknown. To reveal their function in the corneal epithelium, PAX6 isoforms, along with reprogramming factors, were transduced into human non-ocular epithelial cells. Herein, we show that the two PAX6 isoforms differentially and cooperatively regulate the expression of genes specific to the structure and functions of the corneal epithelium, particularly keratin 3 (KRT3) and keratin 12 (KRT12). PAX6 isoform-a induced KRT3 expression by targeting its upstream region. KLF4 enhanced this induction. A combination of PAX6 isoform-b, KLF4 and OCT4 induced KRT12 expression. These new findings will contribute to furthering the understanding of the molecular basis of the corneal epithelium specific phenotype.
Biomechanical Evaluations of Ocular Injury Risk for Blast Loading (2017)

Ocular trauma is one of the most common types of combat injuries resulting from the exposure of military personnel with improvised explosive devices. The injury mechanism associated with the primary blast wave is poorly understood. We employed a three-dimensional computational model, which included the main internal ocular structures of the eye, spatially varying thickness of the cornea-scleral shell, and nonlinear tissue properties, to calculate the intraocular pressure and stress state of the eye wall and internal ocular structure caused by the blast. The intraocular pressure and stress magnitudes were applied to estimate the injury risk using existing models for blunt impact and blast loading. The simulation results demonstrated that blast loading can induce significant stresses in the different components of the eyes that correlate with observed primary blast injuries in animal studies. Different injury models produced widely different injury risk predictions, which highlights the need for experimental studies evaluating mechanical and functional damage to the ocular structures caused by the blast loading.
Temperature-Responsive Nanospheres with Bicontinuous Internal Structures from a Semicrystalline Amphiphilic Block Copolymer (2010)

Internally structured self-assembled nanospheres, cubosomes, are formed from a semicrystalline block copolymer, poly(ethylene oxide)-block-poly(octadecyl methacrylate) (PEO(39)-b-PODMA(17)), in aqueous dispersion. The PODMA block provides them with a temperature-responsive structure and morphology. Using cryo-electron tomography, we show that at room temperature these internally bicontinuous aggregates undergo an unprecedented order-disorder transition of the microphase-separated domains that is accompanied by a change in the overall aggregate morphology. This allows switching between spheres with ordered bicontinuous internal structures at temperatures below the transition temperature and more planar oblate spheroids with a disordered microphase-separated state above the transition temperature. The bicontinuous structures offer a number of possibilities for application as templates, e.g., for biomimetic mineralization or polymerization. Furthermore, the unique nature of the thermal transition observed for this system offers up considerable possibilities for their application as temperature-controlled release vessels.
Inertial-Electrostatic Confinement: An Approach to Burning Advanced Fuels (1991)

Inertial-Electrostatic Confinement (IEC) is currently undergoing renewed experimental and theoretical study as a fusion reactor scheme that can burn advanced fuels such as D-3He and p-11B. The goal of the IEC approach is the confinement of plasma inside multiple nested spherical potential wells. These wells are created by injecting ions into a highly transparent, high voltage (5 – 50 kV) spherical cathode. Multiple passes of ions through the center create a high density non-Maxwellian core.An IEC device can produce intense beam-background (ion-neutral) and beam-beam (ion-ion) fusion reactions with or without the formation of a “Poissor” structure (multiple well). Two different approaches for injecting ions are also under study: ion guns and ionization of background gas. The initial experimental results presented here are taken in the non-Poissor beam-background mode as a precursor to experimentation in the more complex beam-beam and Poissor modes.