gebhart/patrepeval huggingface dataset:
Segmentation of digitized histological sections for quantification of the muscularized vasculature in the mouse hind limb (2017)

Immunohistochemical tissue staining enhances microvasculature characteristics, including the smooth muscle in the medial layer of the vessel walls that is responsible for regulation of blood flow. The vasculature can be imaged in a comprehensive fashion using whole-slide scanning. However, since each such image potentially contains hundreds of small vessels, manual vessel delineation and quantification is not practically feasible. In this work, we present a fully automatic segmentation and vasculature quantification algorithm for whole-slide images. We evaluated its performance on tissue samples drawn from the hind limbs of wild-type mice, stained for smooth muscle using 3,3'-Diaminobenzidine (DAB) immunostain. The algorithm was designed to be robust to vessel fragmentation due to staining irregularity, and artefactual staining of nonvessel objects. Colour deconvolution was used to isolate the DAB stain for detection of vessel wall fragments. Complete vessels were reconstructed from the fragments by joining endpoints of topological skeletons. Automatic measures of vessel density, perimeter, wall area and local wall thickness were taken. The segmentation algorithm was validated against manual measures, resulting in a Dice similarity coefficient of 89%. The relationships observed between these measures were as expected from a biological standpoint, providing further reinforcement of the accuracy of this system. This system provides a fully automated and accurate means of measuring the arteriolar and venular morphology of vascular smooth muscle.
Assay of crystal violet binding for rapid identification of virulent plasmid-bearing clones of Yersinia enterocolitica (1987)

A rapid, reliable, and simple method based on the binding of crystal violet (CV) is described for differentiating virulence-plasmid-bearing strains of Yersinia enterocolitica from their plasmidless derivatives. As with other plasmid-mediated properties of this organism, the binding of CV occurs at 37 degrees C but not at 25 degrees C. The CV-binding technique provides a simple and efficient means of screening Y. enterocolitica for virulence and for identifying individual plasmid-bearing colonies.
Exosome: A Novel and Safer Therapeutic Refinement of Mesenchymal Stem Cell (2013)

Mesenchymal stem cell (MSC) has just been approved as the first “off-the-shelf” stem cell pharmaceutical drug with an anticipation of more approvals following completion of numerous rigorous clinical trials. Despite this progress, the rationale for MSC therapeutic efficacy remains tenuous and is increasingly rationalized on a secretion rather than differentiation mechanism. Recent studies identifying exosome as the secreted agent mediating MSC therapeutic efficacy could potentially reduce a cell-based drug to a safer biologic-based alternative. Here we review the development of MSC exosome as a potential first-in-class therapeutic, and the unique challenges in the manufacture and regulatory oversight of this new class of therapeutics.
Development and Application of Microcapsule for Cosmetics. (1992)

Microcapsules are minute containers in which individual entities of a solid, liquid, or gas are discretely enclosed, with shells made of natural or synthetic materials. These shells may be designed to protect from their environment, to aid in the storage, or to release their contents at specific rate or under a specific set of conditions. In the applications of microcapsules to cosmetics (particularly to cream), it may be necessary for microcapsules to have the following requirements; 1. the transparent shell film . the easy preparation process . insolubility in water or other solvents 4. easy breaking of shells on the palms of the hands upon usage 5. the composition of the innocuous ingredients for a human body. The shell materials and the pre paration methods were studied to satisfy the above requirements. The most suitable microcap sules were prepared by a complex coacervation methods involving a phase separation in a ge latinmacacia mixture in aqueous phase. Their shells were composed of the crosslinked gelatin. G l ut ar ald ehyde was selected as the crosslinkin agent to denature gelatin into an insolble sub stance in water or other solvents. The particle sizes of the developed microcapsules were corn trolled by the stirring rate on preparation or the polarity of the oil enclosed within. Also, the breaking strength of microcapsule was controlled by mixing a liquid and a solid oil com ponent in the suitable ratio. The stabilization of fragrance, vitamin A palmitate and ethyl lino leate was tried by microencapsulation in order to protect the enclosed materials from their environment icroencapsulated substances showed an excellent in stability compared with emulsificated substances. Further, a more excellent stability could be exhibited by increasing the shell thickness of microcapsule or modifying the microcapsule's gelatin film by poly-lysin. From the measurents of the oxygen permeability coefficient of the plane modified eratin film, it was supposed that the fine matrix composed of gelatin and poly-lysin prevented the oxygen permeability and this gave an excellent stability.
Thin-film coatings for flexible optical data storage (1990)

A write-once optical data storage media has been developed which is suitable for tape formats. The recording layer is a metal alloy system which is sputter deposited onto polymeric substrates as a single-layer thin film. The media are manufactured using a continuous sheet process, where the reflectivity of the film at 840nm can be selectively varied between 30 and 70%. These films have been characterized for laser write sensitivity, optical properties, surface chemistry, and environmental stability. An abrasion resistant hard overcoat is applied directly onto the active surface in a second vacuum deposition step. The media performance has been found to be compatible with direct hard-overcoats with no degradation in write sensitivity.
A New Enzyme,<scp>D</scp>-Ketohexose 3-Epimerase, from<i>Pseudomonas</i>sp. ST-24 (1993)

Journal Article A New Enzyme, D-Ketohexose 3-Epimerase, from Pseudomonas sp. ST-24 Get access Ken Izumori, Ken Izumori Department of Bioresource Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761–07, Japan Corresponding author. Search for other works by this author on: Oxford Academic Google Scholar Anisur Rahman Khan, Anisur Rahman Khan Department of Bioresource Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761–07, Japan Search for other works by this author on: Oxford Academic Google Scholar Hiroaki Okaya, Hiroaki Okaya Department of Bioresource Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761–07, Japan Search for other works by this author on: Oxford Academic Google Scholar Tetsuji Tsumura Tetsuji Tsumura Department of Bioresource Science, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa 761–07, Japan Present address: Department of Food Nutrition, Setouchi Junior College, Takase-cho, Mitoyo-gun, Kagawa 767, Japan. Search for other works by this author on: Oxford Academic Google Scholar Bioscience, Biotechnology, and Biochemistry, Volume 57, Issue 6, 1 January 1993, Pages 1037–1039, https://doi.org/10.1271/bbb.57.1037 Published: 01 January 1993 Article history Received: 24 February 1992 Published: 01 January 1993
SecureMed: Secure Medical Computation using GPU-Accelerated Homomorphic Encryption Scheme. (2016)

Sharing the medical records of individuals among healthcare providers and researchers around the world can accelerate advances in medical research. While the idea seems increasingly practical due to cloud data services, maintaining patient privacy is of paramount importance. Standard encryption algorithms help protect sensitive data from outside attackers but they cannot be used to compute on this sensitive data while being encrypted. Homomorphic Encryption (HE) presents a very useful tool that can compute on encrypted data without the need to decrypt it. In this work, we describe an optimized NTRUbased implementation of the GSW homomorphic encryption scheme. Our results show a factor of 58× improvement in CPU performance compared to other recent work on encrypted medical data under the same security settings. Our system is built to be easily portable to GPUs resulting in an additional speedup of up to a factor of 104× (and 410×) to offer an overall speedup of 6085× (and 24011×) using a single GPU (or four GPUs), respectively.
Rewriting queries on SPARQL views (2011)

The problem of answering SPARQL queries over virtual SPARQL views is commonly encountered in a number of settings, including while enforcing security policies to access RDF data, or when integrating RDF data from disparate sources. We approach this problem by rewriting SPARQL queries over the views to equivalent queries over the underlying RDF data, thus avoiding the costs entailed by view materialization and maintenance. We show that SPARQL query rewriting combines the most challenging aspects of rewriting for the relational and XML cases: like the relational case, SPARQL query rewriting requires synthesizing multiple views; like the XML case, the size of the rewritten query is exponential to the size of the query and the views. In this paper, we present the first native query rewriting algorithm for SPARQL. For an input SPARQL query over a set of virtual SPARQL views, the rewritten query resembles a union of conjunctive queries and can be of exponential size. We propose optimizations over the basic rewriting algorithm to (i) minimize each conjunctive query in the union; (ii) eliminate conjunctive queries with empty results from evaluation; and (iii) efficiently prune out big portions of the search space of empty rewritings. The experiments, performed on two RDF stores, show that our algorithms are scalable and independent of the underlying RDF stores. Furthermore, our optimizations have order of magnitude improvements over the basic rewriting algorithm in both the rewriting size and evaluation time.
Spectral and modulation performance of quantum cascade lasers with application to remote sensing (1999)

We have characterized the spectral noise density and frequency modulation performance of an 8.5 micron quantum- cascade diode (QC) laser operating continuously at liquid nitrogen temperatures. The phase noise is measured by fixing the laser frequency in the half-height region of a molecular resonance and measuring the fluctuations in absorbance; these fluctuations are then accurately converted into measurements in the fluctuations of the absolute frequency. A Fourier analysis of the intrinsic spectral/phase noise show a 1/f2 dependence up to the measurement bandwidth limit of approximately 1 MHz. The laser linewidth is < 1 MHz when measured over several milliseconds. Servo locking schemes will be discussed with the implication that QC laser sources can be stabilized to a high degree. The frequency modulation performance of a QC laser has been measured and synchronous detection of f, 2f and 3f absorption signals (nitrous oxide at 8.5 micrometers ) has been achieved with direct modulation of the injection current.© (1999) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
52.4: Highly Efficient Single‐Unit White OLED Device with Emission from Both Singlet and Triplet Excitons (2014)

Abstract We succeeded in developing a single‐unit hybrid organic light‐emitting diode (OLED) device with efficient light emission from both a phosphorescent layer and a fluorescent layer. The single‐unit hybrid OLED achieved power efficiency higher than that of a two‐unit hybrid tandem OLED with a phosphorescent and fluorescent layers.
POSTTRANSPLANT THERAPY USING HIGH-DOSE HUMAN IMMUNOGLOBULIN (INTRAVENOUS GAMMAGLOBULIN) TO CONTROL ACUTE HUMORAL REJECTION IN RENAL AND CARDIAC ALLOGRAFT RECIPIENTS AND POTENTIAL MECHANISM OF ACTION1 (1998)

I.v.IG appears to be an effective therapy to control posttransplant AR episodes in heart and kidney transplant recipients, including patients who have had no success with conventional therapies. Vascular rejection episodes associated with development of donor-specific cytotoxic antibodies appears to be particularly responsive to i.v.IG therapy.
<title>Modeling of master oscillator-power amplifier (MOPA) semiconductor lasers</title> (1997)

Monolithically integrated flared amplifier master oscillator power amplifier (MFA-MOPA) semiconductor lasers are studied theoretically using a high resolution computational model which resolved times and longitudinal and transverse space dependencies and includes Lorentzian gain and dispersion spectra. The simulations show that, by altering the linear flare of the power amplifier into a nonlinear, trumpet- shaped flare, the dynamic stability range of the MOPA is increased by a factor of 3. This enables the MOPA to maintain a stable, nearly diffraction limited output beam for higher currents before the onset of transverse instabilities, large beam divergence and facet damage due to filamentation. Thus the MOPA will be able to emit an output beam of significantly higher power and brightness.
Abstract 19204: Characteristics of Chest Compressions Immediately Before and After Interruptions During Pediatric In-hospital CPR (2017)

Introduction: High-quality CPR, with chest compressions (CC) of optimal rate and depth, improves cardiac arrest survival. CPR quality has not been characterized immediately before and after interru...
Rare Exonic Minisatellite Alleles in MUC2 Influence Susceptibility to Gastric Carcinoma (2007)

Our observations suggest that the short rare MUC2-MS6 alleles could function as identifiers for risk of gastric cancer. Additionally, we suggest that minisatellite instability might be associated with MUC2 function in cancer cells.
A Fast Algorithm for Searching for Molecules Containing a Pharmacophore in Very Large Virtual Combinatorial Libraries (2001)

We present a new algorithm for identifying molecules that display a pharmacophore, or in general a structural motif, by efficiently constructing and screening huge virtual combinatorial libraries of diverse compounds. The uniqueness of this algorithm is its ability to build and screen libraries of ca. 10(18) 3D molecular conformations within a reasonable time scale, thereby increasing the chemical space that can be virtually screened by many orders of magnitude. The algorithm may be used to design new molecules that display a desired pharmacophore on predefined sets of chemical scaffolds. This is demonstrated herein by screening a library of backbone cyclic peptides to find candidate peptido- and proteinomimetics.
A Candida albicans Strain Expressing Mammalian Interleukin-17A Results in Early Control of Fungal Growth during Disseminated Infection (2015)

Candida albicans is normally a commensal fungus of the human mucosae and skin, but it causes life-threatening systemic infections in hospital settings in the face of predisposing conditions, such as indwelling catheters, abdominal surgery, or antibiotic use. Immunity to C. albicans involves various immune parameters, but the cytokine interleukin-17A (IL-17A) (also known as IL-17) has emerged as a centrally important mediator of immune defense against both mucosal and systemic candidiasis. Conversely, IL-17A has been suggested to enhance the virulence of C. albicans, indicating that it may exert detrimental effects on pathogenesis. In this study, we hypothesized that a C. albicans strain expressing IL-17A would exhibit reduced virulence in vivo. To that end, we created a Candida-optimized expression cassette encoding murine IL-17A, which was transformed into the DAY286 strain of C. albicans. Candida-derived IL-17A was indistinguishable from murine IL-17A in terms of biological activity and detection in standard enzyme-linked immunosorbent assays (ELISAs). Expression of IL-17A did not negatively impact the growth of these strains in vitro. Moreover, the IL-17A-expressing C. albicans strains showed significantly reduced pathogenicity in a systemic model of Candida infection, mainly evident during the early stages of disease. Collectively, these findings suggest that IL-17A mitigates the virulence of C. albicans.
Up-regulating pyocyanin production by amino acid addition for early electrochemical identification of Pseudomonas aeruginosa (2014)

This work focuses on developing a faster method for electrochemically detecting a Pseudomonas aeruginosa infection through the addition of amino acids to cell culture samples. We performed square-wave voltammetry measurements of pyocyanin produced by P. aeruginosa using commercially available carbon-based electrodes connected to a Ag/AgCl reference. The electrochemical response resulting from the production of pyocyanin by bacteria was measured in the presence of various amino acids while varying three different culturing parameters: liquid media type (trypticase soy broth vs. M63 minimal media); concentration of amino acids in the solution; and initial concentration of the P. aeruginosa in the solution. Our results demonstrate a faster and stronger electrochemical response in media containing tyrosine and valine at elevated concentrations, lending promise to using amino acids as up-regulatory molecules for faster bacterial detection.
Optimization of peptide substrates for botulinum neurotoxin E improves detection sensitivity in the Endopep–MS assay (2014)

Botulinum neurotoxins (BoNTs) produced by Clostridium botulinum are the most poisonous substances known to humankind. It is essential to have a simple, quick, and sensitive method for the detection and quantification of botulinum toxin in various media, including complex biological matrices. Our laboratory has developed a mass spectrometry-based Endopep-MS assay that is able to rapidly detect and differentiate all types of BoNTs by extracting the toxin with specific antibodies and detecting the unique cleavage products of peptide substrates. Botulinum neurotoxin type E (BoNT/E) is a member of a family of seven distinctive BoNT serotypes (A-G) and is the causative agent of botulism in both humans and animals. To improve the sensitivity of the Endopep-MS assay, we report here the development of novel peptide substrates for the detection of BoNT/E activity through systematic and comprehensive approaches. Our data demonstrate that several optimal peptides could accomplish 500-fold improvement in sensitivity compared with the current substrate for the detection of both not-trypsin-activated and trypsin-activated BoNT/E toxin complexes. A limit of detection of 0.1 mouse LD50/ml was achieved using the novel peptide substrate in the assay to detect not-trypsin-activated BoNT/E complex spiked in serum, stool, and food samples.
<i>Manduca sexta</i> (Lepidoptera: Sphingidae) cadherin fragments function as synergists for Cry1A and Cry1C <i>Bacillus thuringiensis</i> toxins against noctuid moths <i>Helicoverpa zea, Agrotis ipsilon</i> and <i>Spodoptera exigua</i> (2009)

The commercial development of this synergist has the potential to widen the spectrum of Bt toxicity to other important agricultural lepidopteran insect pests and thus increase its usefulness in agriculture.
Evaluation of Intravitreal Aflibercept for the Treatment of Severe Nonproliferative Diabetic Retinopathy (2021)

ClinicalTrials.gov Identifier: NCT02718326.
A Novel Framework for Threat Analysis of Machine Learning-based Smart Healthcare Systems (2021)

Smart healthcare systems (SHSs) are providing fast and efficient disease treatment leveraging wireless body sensor networks (WBSNs) and implantable medical devices (IMDs)-based internet of medical things (IoMT). In addition, IoMT-based SHSs are enabling automated medication, allowing communication among myriad healthcare sensor devices. However, adversaries can launch various attacks on the communication network and the hardware/firmware to introduce false data or cause data unavailability to the automatic medication system endangering the patient's life. In this paper, we propose SHChecker, a novel threat analysis framework that integrates machine learning and formal analysis capabilities to identify potential attacks and corresponding effects on an IoMT-based SHS. Our framework can provide us with all potential attack vectors, each representing a set of sensor measurements to be altered, for an SHS given a specific set of attack attributes, allowing us to realize the system's resiliency, thus the insight to enhance the robustness of the model. We implement SHChecker on a synthetic and a real dataset, which affirms that our framework can reveal potential attack vectors in an IoMT system. This is a novel effort to formally analyze supervised and unsupervised machine learning models for black-box SHS threat analysis.
Development of a Family of Redox-Sensitive Green Fluorescent Protein Indicators for Use in Relatively Oxidizing Subcellular Environments (2008)

Green fluorescent protein (GFP) indicators were previously developed that rapidly and quantitatively respond to changes in the thiol/disulfide equilibrium within subcellular compartments. In these indicators, surface-exposed cysteines residues were introduced so as to form a labile redox-active disulfide that in turn controls the emission properties of the internal chromophore. The biosensors have been shown to be effective reporters of the thiol/disulfide status within reducing compartments such as the mitochondria and cytosol for several cell types. However, due to the high thermodynamic stability of the introduced disulfide bond, the indicators are not useful for quantitative analysis within more oxidizing compartments such as the endoplasmic reticulum. Here we report the development of a new family of GFP-based redox indicators (roGFP1-iX) in which the thermodynamic stability of the disulfide is substantially lowered by insertion of a single amino acid into the main chain, adjacent to cysteine 147. The insertions result in indicators with midpoint potentials of -229 to -246 mV and are thus better suited for study of relatively oxidizing subcellular compartments. Atomic resolution crystallographic analyses suggest that two important factors act to destabilize the disulfide linkage in roGFP1-iX. In the oxidized state, an unusual non-proline cis-peptide bond adjacent to one of the cysteines introduces geometric strain into the system, while in the reduced state, a dramatic loop opening lowers the effective concentration of the reacting species.
Low-leakage asymmetric-cell SRAM (2003)

We introduce a novel family of asymmetric dual-V/sub t/ static random access memory cell designs that reduce leakage power in caches while maintaining low access latency. Our designs exploit the strong bias toward zero at the bit level exhibited by the memory value stream of ordinary programs. Compared to conventional symmetric high-performance cells, our cells offer significant leakage reduction in the zero state and, in some cases, also in the one state, albeit to a lesser extent. A novel sense amplifier, in combination with dummy bitlines, allows for read times to be on par with conventional symmetric cells. With one cell design, leakage is reduced by 7/spl times/ (in the zero state) with no performance degradation, but with a stability degradation of 6%. Another cell design reduces leakage by 2/spl times/ (in the zero state) with no performance or stability loss. An alternative cell design reduces leakage by 58/spl times/ (in the zero state) with a performance degradation of 1% and an area increase of 2.4% and no stability degradation.