gebhart/patrepeval huggingface dataset:
Rapid Generation of Biologically Relevant Hydrogels Containing Long‐Range Chemical Gradients (2009)

Many biological processes are regulated by gradients of bioactive chemicals. Thus, the generation of materials with embedded chemical gradients may be beneficial for understanding biological phenomena and generating tissue-mimetic constructs. Here we describe a simple and versatile method to rapidly generate materials containing centimeter-long gradients of chemical properties in a microfluidic channel. The formation of chemical gradient was initiated by a passive-pump-induced forward flow and further developed during an evaporation-induced backward flow. The gradient was spatially controlled by the backward flow time and the hydrogel material containing the gradient was synthesized via photopolymerization. Gradients of a cell-adhesion ligand, Arg-Gly-Asp-Ser (RGDS), was incorporated in the poly(ethylene glycol)-diacrylate (PEG-DA) hydrogels to test the response of endothelial cells. The cells attached and spread along the hydrogel material in a manner consistent with the RGDS gradient profile. A hydrogel containing PEG-DA concentration gradient and constant RGDS concentration was also generated. The morphology of cells cultured on such hydrogel changed from round in the lower PEG-DA concentration regions to well-spread in the higher PEG-DA concentration regions. This approach is expected to be a valuable tool to investigate the cell-material interactions in a simple and high-throughput manner and to design graded biomimetic materials for tissue engineering applications.
Lecture Notes on Network Information Theory (2010)

These lecture notes have been converted to a book titled Network Information Theory published recently by Cambridge University Press. This book provides a significantly expanded exposition of the material in the lecture notes as well as problems and bibliographic notes at the end of each chapter. The authors are currently preparing a set of slides based on the book that will be posted in the second half of 2012. More information about the book can be found at http://www.cambridge.org/9781107008731/. The previous (and obsolete) version of the lecture notes can be found at http://arxiv.org/abs/1001.3404v4/.
Cytokine RNA In Situ Hybridization Permits Individualized Molecular Phenotyping in Biopsies of Psoriasis and Atopic Dermatitis (2021)

Detection of individual cytokines in routine biopsies from patients with inflammatory skin diseases has the potential to personalize diagnosis and treatment selection, but this approach has been limited by technical feasibility. We evaluate whether a chromogen-based RNA in situ hybridization approach can be used to detect druggable cytokines in psoriasis and atopic dermatitis. A series of psoriasis (n = 20) and atopic dermatitis (n = 26) biopsies were stained using RNA in situ hybridization for <i>IL4</i>, <i>IL12B</i> (IL-12/23 p40), <i>IL13</i>, <i>IL17A</i>, <i>IL17F, IL22</i>, <i>IL23A</i> (IL-23 p19), <i>IL31</i>, and <i>TNF</i> (TNF-α). <i>NOS2</i> and <i>IFNG</i>, canonical psoriasis biomarkers, were also included. All 20 of the psoriasis cases were positive for <i>IL17A</i>, which tended to be the predominant cytokine, although some cases had relatively higher levels of <i>IL12B</i>, <i>IL17F,</i> or <i>IL23A</i>. The majority of cytokine expression in psoriasis was epidermal. A total of 22 of 26 atopic dermatitis cases were positive for <i>IL13</i>, also at varying levels; a subset of cases had significant <i>IL4, IL22, or IL31</i> expression. Patterns were validated in independent bulk RNA-sequencing and single-cell RNA-sequencing datasets. Overall, RNA in situ hybridization for cytokines appears highly specific with virtually no background staining and may allow for individualized evaluation of treatment-relevant cytokine targets in biopsies from patients with inflammatory skin disorders.
Field-effect transistors based on a polycyclic aromatic hydrocarbon core as a two-dimensional conductor (2005)

Hexabenzocoronene (HBC) derivatives which are designed to self-assemble into a two-dimensional conductor have been synthesized. The derivatives were deposited by vacuum sublimation as an active layer in organic field-effect transistors. The dihexyl and tetrahexyl derivatives increased the field-effect mobilities and on∕off ratios by a factor of 10 or more as compared to the unsubstituted hexabenzocoronene and the hexahexyl derivative. This good performance could be explained by the self-assembly in a two-dimensional conductor of the HBC derivatives, i.e., the dihexyl and tetrahexyl derivatives, in contrast to the self-assembly in the one-dimensional conductor of the hexahexyl derivative and low self-assembling property of the unsubstituted HBC.
[A new algorithm for displaying the cutting isosurface of structures]. (2001)

The existing algorithms for displaying the cutting isosurface of the structure are not suitable for interactive display because they spend too much time on calculation when a fair amount of data is submitted to processing. This paper presents a new algorithm for accelerating the cutting of structure by using the area partition and the increment calculation to reduce the unnecessary calculation in cutting the structure. It is suitable for real time interactive displaying, especially in the case of a vast amount of data.
Growth and Biochemical Markers of Growth in Children With Snoring and Obstructive Sleep Apnea (2002)

These observations indicate that growth hormone secretion is impaired in children with OSAS and PS. Respiratory improvement after adenotonsillectomy in children with OSAS results in weight gain and restored growth hormone secretion.
Clean and efficient synthesis of azo dyes using polymer-supported reagents (2000)

The first page of this article is displayed as the abstract.
Direct Observation of Crystal-Originated Particles on Czochralski-Grown Silicon Wafer Surface and Effect on Gate Oxide Reliability (1996)

We found that crystal-originated particles (COP) on a Czochralski-grown Si wafer surface consist of single pits and pair pits, using a pattern-defect inspection machine and SEM. The influence of these pits on the gate oxide reliability was studied by means of a time dependent dielectric breakdown (TDDB) test under constant voltage stress (8 MV/cm). It was clearly demonstrated that when the gate oxide thickness was around 10 nm, in the active region pair pits caused gate oxide failure, while single pits did not. It was also found that broad pair pits, formed by preferential oxidation/etching treatment, did not degrade the gate oxide reliability even when situated in the active region.
Robotic Anterior Pelvic Exenteration for Bladder Cancer in the Female: Outcomes and Comparisons to Their Male Counterparts (2008)

In our experience, the robotic anterior exenteration has been readily adapted to the surgical treatment of bladder cancer with similar outcomes to those observed in male patients undergoing a robotic radical cystoprostatectomy. The approach appears to achieve the clinical and oncologic goals of radical cystectomy in both the female and male patient.
Spectro-temporal encoded multiphoton microscopy and fluorescence lifetime imaging at kilohertz frame-rates (2020)

Two-Photon Microscopy has become an invaluable tool for biological and medical research, providing high sensitivity, molecular specificity, inherent three-dimensional sub-cellular resolution and deep tissue penetration. In terms of imaging speeds, however, mechanical scanners still limit the acquisition rates to typically 10-100 frames per second. Here we present a high-speed non-linear microscope achieving kilohertz frame rates by employing pulse-modulated, rapidly wavelength-swept lasers and inertia-free beam steering through angular dispersion. In combination with a high bandwidth, single-photon sensitive detector, this enables recording of fluorescent lifetimes at speeds of 88 million pixels per second. We show high resolution, multi-modal - two-photon fluorescence and fluorescence lifetime (FLIM) - microscopy and imaging flow cytometry with a digitally reconfigurable laser, imaging system and data acquisition system. These high speeds should enable high-speed and high-throughput image-assisted cell sorting.
NK Cells Influence Both Innate and Adaptive Immune Responses after Mucosal Immunization with Antigen and Mucosal Adjuvant (2010)

NK cells were found to be recruited in a temporally controlled manner to the nasal-associated lymphoid tissue and the cervical lymph nodes of mice after intranasal immunization with Ag85B-early secreted antigenic target 6 kDa from Mycobacterium tuberculosis mixed with Escherichia coli heat-labile toxin as adjuvant. These NK cells were activated and secreted a diverse range of cytokines and other immunomodulators. Using Ab depletion targeting anti-asialo GM1, we found evidence for altered trafficking, impaired activation, and cytokine secretion of dendritic cells, macrophages, and neutrophils in immunized NK cell-depleted mice compared with control animals. Analysis of Ag-specific immune responses revealed an attenuated Ab and cytokine response in immunized NK cell-depleted animals. Systemic administration of rIL-6 but not rIFN-gamma significantly restored immune responses in mice depleted of NK cells. In conclusion, cytokine production, particularly IL-6, via NK cells and NK cell-activated immune populations plays an important role in the establishment of local innate immune responses and the consequent development of adaptive immunity after mucosal immunization.
Unsteady Normal Shock Wave Boundary Layer Interactions with Control (2008)

An experimental study of a normal shock wave subject to unsteady periodic forcing in a parallel walled duct has been conducted. The dynamics of shock motion have been analysed and a simple theoretical model describing the periodic shock motion has been produced. A non-dimensional relationship between the amplitude and frequency of shock motion in a diverging duct has been outlined, based on the concept of a critical frequency relating the relative importance of geometry and disturbance frequency on shock dynamics. This inviscid analysis breaks down when the shock is subjected to high accelerations, as the flnite time needed for changes in the boundary layer structure due to shock motion to occur become signiflcant and begin to in∞uence shock dynamics. The boundary layer is also thought to play a critical role in the upstream transmission of pressure information to the shock. It is concluded that although some aspects of unsteady shock dynamics can be predicted using a simple inviscid model, such a model does not capture the true physics of the ∞ow, which must be in∞uenced by viscosity. Experiments using ∞ow control to modify the viscous properties of the boundary layer have been conducted, although preliminary results have shown that the control has no noticeable efiects on shock dynamics. However, this is attributed to limitations in the current experiments and further experiments with control are proposed.
Molecular cloning and restriction endonuclease mapping of the glutamate synthase gene from salt-tolerant Bradyrhizobium spp. strain WR1001 (1999)

In order to clone the glutamate synthase gene (glt) from salt-tolerant Bradyrhizobium spp. strain WR1001, a genomic cosmid library was constructed using the vector pHC79. The library was mass-conjugated into Escherichia coli ET1194 (glt−) in a triparental mating, using pRK2013 as a mobilizing plasmid. Transconjugants of ET1194 which grew on minimal medium and had Glt+ phenotype were selected for the isolation of recombinant cosmids. Plasmid pHL27, which contained a 40-kb insert of WR1001 DNA and complemented ET1194 to Glt+ phenotype, was chosen to delimit the glutamate synthase gene. The region that encoded glt in cosmid pHL27 was determined by Southern blot analysis using the cloned glt gene of E. coli DH1 as a probe. An 11-kb HindIII DNA fragment from pHL27 contained the fully functional glt gene. Partial PstI and EcoRI restriction enzyme digests of cosmid pHL27 were subcloned into the vectors pBS+ and pUC8 and transformed into ET1194 to test for Glt+ phenotype. The glt coding region was defined by aligning the physical maps of the subclones
Investigation of the High Temperature Shift for a Generation of High Purity Hydrogen (2008)

The generation of high-purity hydrogen from hydrocarbon fuels is essential for efficient operation of fuel cell. In general, most feasible strategies to generate hydrogen from hydrocarbon fuels consist of a reforming step to generate a mixture of H2, CO, CO2 and H2O (steam) followed by water gas shift (WGS) and CO clean-up steps. The WGS reaction that shifts CO to CO2 and simultaneously produces another mole of H2 was carried out in a two-stage catalytic conversion process involving a high temperature shift (HTS) and a low temperature shift (LTS). In a typical operation, gas emerges from the reformer is taken through a high temperature shift catalyst to reduce the CO concentration to about 3∼5%. The HTS reactor was designed and tested in this study to produce hydrogen-rich gas with CO to a range of 2∼4%. The iron based catalysts (G-3C) was used for the HTS to convert the most of CO in the effluent from the partial oxidation (POX) to H2 and CO2 at a relatively high rate. Parametric screening studies were carried out for variations of the following variables: reaction temperature, steam flow rate, components ratio (H2/CO), and reforming gas flow rate.
Ferroelectric film switching via oblique domain growth observed by cross-sectional nanoscale imaging (2006)

Different stages of polarization reversal in a Pb(Zr,Ti)O3 ferroelectric film have been directly observed using a technique of cross-sectional piezoelectric force imaging. Analysis of the local piezoelectric response measured across the cross section strongly suggests that polarization reversal occurs via oblique domain growth rather than by growth of domains perpendicular to the film plane. The proposed approach represents a valuable extension to the piezoelectric force microscopy (PFM) and contributes to a better understanding of results observed using more standard techniques. Particularly, oblique domain growth explains the gradual variation of piezoelectric response amplitude commonly observed in planar PFM images.
103Pd versus 125I ophthalmic plaque brachytherapy: preoperative comparative radiation dosimetry for 319 uveal melanomas (2014)

Preoperative comparative radiation dosimetry was performed for a large cohort of patients with uveal melanoma. It influenced radionuclide selection, offered an opportunity for radiation sparing of critical vision-related intraocular structures, and typically increased radiation within the tumors.
Fabrication of Submicrometer Period Gratings with Precisely Defined Profiles for Integrated Optics Applications* (1980)

Several integrated optics devices require precisely defined gratings with submicrometer periodicities. These include distributed feedback lasers, filters, resonators, input-output couplers, etc. Two recently developed techniques [1,2] for fabricating grating structures will be described together with the application of these techniques in the field of integrated optics.
CLINICAL EFFECTIVENESS OF TRANS-ARTICULAR VERSUS RETRO-ARTICULAR DRILLING OF STABLE OSTEOCHONDRITIS DISSECANS OF THE KNEE: A, PROSPECTIVE RANDOMIZED CONTROLLED TRIAL BY THE ROCK STUDY GROUP (2021)

Background: The most common presentation of knee osteochondritis dissecans (OCD) is a stable lesion on the lateral aspect of the medial femoral condyle (MFC) in an adolescent or pre-adolescent athlete. Standard of care for conservative treatment, include activity modification and weight bearing protection. Failed conservative management often leads arthroscopy and drilling of the lesion. Two different primary drilling techniques have been utilized, but no prospective studies have compared their relative effectiveness. Hypothesis/Purpose: The study hypothesis was that trans-articular (TAD) and retro-articular drilling (RAD) would demonstrate similar rates of healing, times to return to sports, and patient-reported outcome scores (PROs). Methods: Skeletally immature (n=113) patients presenting with radiograph indicated stable OCD of the MFC who did not demonstrate healing despite a minimum of 3 months of non-operative treatment were prospectively enrolled and randomized to TAD or RAD, for which 17 surgeon-investigators (at 14 centers, representing all major regions in the U.S.). Serial radiographs were obtained every 6 weeks to assess healing, and PROs were obtained at 6 months, 12 months, and 24 months. Twelve patients were due to lesion instability detected at the time of surgery, Results: Ninety-one study subjects were included, consisting of 51 TAD and 40 RAD patients, with the two groups being of similar age (12.6 years vs. 11.9 years), sex distribution (45% vs. 27% female, p=0.081), and 2-year PRO response rate (both 90%). No significant difference between TAD and RAD was detected in follow-up Pedi-IKDC, Lysholm, Marx knee activity score, or KOOS QOL scores (Table 1). Revision/additional OCD surgery occurred in 10% of patients in RAD and 4% in TAD. 71% of TAD patients reached a ‘healed’ status at a mean of 1.15 years, compared with 58% RAD patients at a mean of 1.06 years. Conclusion: While both primary forms of OCD drilling (TAD and RAD) showed consistent post-operative healing, achieving a completely ‘healed’ status was often a more prolonged process, taking approximately 1 year, despite clinical improvement being achieved much sooner. While PROs were similar between drilling techniques, revision surgery rates were more than twice as common with RAD compared with TAD but the overall risk was low and the Absolute Risk was only 6%. [Table: see text]
A Full-Duplex, Single-Frequency-Controlled Phased Array (2006)

A full-duplex frequency-controlled phased array is demonstrated. Scanning is achieved through the use of a single VCO without any change in the radiated frequency. A compact, novel feed network is designed to distribute the VCO signal to a set of heterodyne mixers. Patterns in both transmit and receive mode demonstrate 40deg of scanning
Linear array characteristics with one-dimensional reactive-region near-field scanning: simulations and measurements (1991)

A model for simulating the performance of a phased-array antenna with one-dimensional near-field scanning is addressed. Measurements and simulations in the reactive near-field region for a linear array with monopole elements are described. The array and near-field probe characteristics are simulated by using the method of moments. Measurements and simulations of the array near-zone received voltage, plane-wave spectrum, and far-field data, using centerline scanning at less than one wavelength distance from the antenna, are shown to be in good agreement. The presence of evanescent grating lobes in the plane-wave spectrum is observed. It is shown that a V-dipole theoretical probe antenna can accurately model a practical near-field measurement probe.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Increased expression of 72-kd type IV collagenase (MMP-2) in human aortic atherosclerotic lesions. (1996)

MMP-2, a secreted 72-kd metalloproteinase that specifically degrades type IV collagen as well as denatured collagens, has been implicated in smooth muscle cell migration. To evaluate the possible contribution of this enzyme to the formation and progression of the atherosclerotic lesion, the expression of MMP-2 was studied in human aortic tissue. MMP-2 was visualized in frozen sections of the aortic wall by an immunofluorescent technique with a polyclonal antibody. Expression of MMP-2 in the aortic extracts was also studied by zymography and Western blotting. Our results reveal that a greater amount of MMP-2 is present in fatty streaks and atherosclerotic plaques as compared with normal regions of the aorta. Immunoblotting analysis showed that MMP-2 was expressed in atherosclerotic plaque > fatty streak > normal aortic wall in a ratio of approximately 4:2:1. Zymograms show that both forms (activated and latent) of MMP-2 increased in the atherosclerotic plaques. The presence of macrophages, detected by an immunohistochemical technique in some areas of higher MMP-2 expression suggests that these cells are a possible source of MMP-2. We conclude that MMP-2 collagenase may have a role in the formation and progression of the atherosclerotic lesion and may be involved in clinical complications of atherosclerosis, such as fissure and rupture, leading to thrombosis.
Transform Coding Techniques for Lossy Hyperspectral Data Compression (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Transform-based lossy compression has a huge potential for hyperspectral data reduction. Hyperspectral data are 3-D, and the nature of their correlation is different in each dimension. This calls for a careful design of the 3-D transform to be used for compression. In this paper, we investigate the transform design and rate allocation stage for lossy compression of hyperspectral data. First, we select a set of 3-D transforms, obtained by combining in various ways wavelets, wavelet packets, the discrete cosine transform, and the Karhunen–Loève transform (KLT), and evaluate the coding efficiency of these combinations. Second, we propose a low-complexity version of the KLT, in which complexity and performance can be balanced in a scalable way, allowing one to design the transform that better matches a specific application. Third, we integrate this, as well as other existing transforms, in the framework of Part 2 of the Joint Photographic Experts Group (JPEG) 2000 standard, taking advantage of the high coding efficiency of JPEG 2000, and exploiting the interoperability of an international standard. We introduce an evaluation framework based on both reconstruction fidelity and impact on image exploitation, and evaluate the proposed algorithm by applying this framework to AVIRIS scenes. It is shown that the scheme based on the proposed low-complexity KLT significantly outperforms previous schemes as to rate-distortion performance. As for impact on exploitation, we consider multiclass hard classification, spectral unmixing, binary classification, and anomaly detection as benchmark applications. </para>
An improved unbiased method for diffspect quantification in epilepsy (2009)

Determining the region of seizure onset is of critical importance for treating medically intractable epilepsy. Comparisons between an ictal and interictal Single Photon Emission Computed Tomography (SPECT) images have been shown to be successful in localizing focal epilepsy. The Ictal-Interictal Subtraction Analysis by Statistical Parametric Mapping (ISAS) algorithm remains one the more successful algorithms for comparing these images. However ISAS is limited by its statistical design. This design introduces a scan order bias in the estimation of the normal variance of sequential SPECT images. We have corrected this bias by estimating the normal variance with a half-normal distribution. In this paper we present an updated algorithm (ISAS HN) based on the original ISAS algorithm with a corrected estimate of the normal variance and an open-source utility for ISAS HN.