gebhart/patrepeval huggingface dataset:
An Engineered Knottin Peptide Labeled with18F for PET Imaging of Integrin Expression (2009)

Knottins are small constrained polypeptides that share a common disulfide-bonded framework and a triple-stranded beta-sheet fold. Previously, directed evolution of the Ecballium elaterium trypsin inhibitor (EETI-II) knottin led to the identification of a mutant that bound to tumor-specific alpha(v)beta(3) and alpha(v)beta(5) integrin receptors with low nanomolar affinity. The objective of this study was to prepare and evaluate a radiofluorinated version of this knottin (termed 2.5D) for microPET imaging of integrin positive tumors in living subjects. Knottin peptide 2.5D was prepared by solid-phase synthesis and folded in vitro, and its free N-terminal amine was reacted with N-succinimidyl-4-18/19F-fluorobenzoate (18/19F-SFB) to produce the fluorinated peptide 18/19F-FB-2.5D. The binding affinities of unlabeled knottin peptide 2.5D and 19F-FB-2.5D to U87MG glioblastoma cells were measured by competition binding assay using 125I-labeled echistatin. It was found that unlabeled 2.5D and 19F-FB-2.5D competed with 125I-echistatin for binding to cell surface integrins with IC(50) values of 20.3 +/- 7.3 and 13.2 +/- 5.4 nM, respectively. Radiosynthesis of 18F-FB-2.5D resulted in a product with high specific activity (ca. 100 GBq/micromol). Next, biodistribution and positron emission tomography (PET) imaging studies were performed to evaluate the in vivo behavior of 18F-FB-2.5D. Approximately 3.7 MBq 18F-FB-2.5D was injected into U87MG tumor-bearing mice via the tail vein. Biodistribution studies demonstrated that 18F-FB-2.5D had moderate tumor uptake at 0.5 h post injection, and coinjection of a large excess of the unlabeled peptidomimetic c(RGDyK) as a blocking agent significantly reduced tumor uptake (1.90 +/- 1.15 vs 0.57 +/- 0.14%ID/g, 70% inhibition, P < 0.05). In vivo microPET imaging showed that 18F-FB-2.5D rapidly accumulated in the tumor and quickly cleared from the blood through the kidneys, allowing excellent tumor-to-normal tissue contrast to be obtained. Collectively, 18F-FB-2.5D allows integrin-specific PET imaging of U87MG tumors with good contrast and further demonstrates that knottins are excellent peptide scaffolds for development of PET probes with potential for clinical translation.
P3‐083: DEVELOPMENT OF COGNITIVE LEVEL ESTIMATION MODEL USING MOBILE APPLICATIONS (2019)

It is important to detect a decline of cognitive level at early stages, because it leads to early treatment, slowdown the progression, and recovery to healthy state. In most cases, however, medical inspection is being done after the person or his/her surroundings notice the symptom of the decline. We can expect to detect the decline of cognitive level at early stages if we can measure the cognitive level by utilizing information obtained from operational logs of a smartphone. The purpose of this study is to figure out if we could estimate the cognitive level with simple quizzes on a smartphone. 154 subjects, aged 56–88 years, participated in this study. The subjects were divided into 3 cognitive level groups (healthy controls (HC), mild cognitive impairment (MCI) and early stage Alzheimer disease (AD)) based on the results of mini mental state examination (MMSE), clinical dementia rating (CDR), geriatric depression scale (GDS) and MRI or CT image investigation for MCI and AD subjects. We built a logistic regression model to estimate cognitive level utilizing operational logs of quizzes on smartphones. By utilizing the logistic regression model, we found that their cognitive levels could be estimated with score and response time of the quizzes. The sensitivity and specificity for healthy people were 0.86 and 0.94 respectively, those for MCI were 0.78 and 0.76 respectively, and those for dementia people were 0.69 and 0.90 respectively. These results suggested that the cognitive level can be estimated with an operational log of quizzes on a smartphone. This means that we can detect the decline of the cognitive level at early stages by utilizing a smartphone in daily lives.
Stable Immobilization of Size‐Controlled Bimetallic Nanoparticles in Photonic Crystal Fiber Microreactor (2018)

Abstract The possibility of immobilizing ex situ‐synthesized colloidal bimetallic nanoparticles (NPs) of well‐defined characteristics inside hollow core photonic crystal fiber (HC‐PCF) microreactors is demonstrated. With the developed method, PtNi clusters remain strongly attached to the fiber core and can be used as active catalysts for the hydrogenation of an azobenzene dye. The study revealed that optical transmission exhibits a size‐dependent behavior, i.e., smaller NPs bring in less optical signal loss. Sufficient light transmission was achieved for all particle sizes. Furthermore, with these catalytic PCF microreactors, kinetic data can be obtained with a much lower amount of precious metals compared to a conventional batch reactor, opening a new pathway for in situ catalyst screening.
INTRAPLEURAL LOW-MOLECULAR-WEIGHT UROKINASE OR TISSUE PLASMINOGEN ACTIVATOR VERSUS SINGLE-CHAIN UROKINASE IN TETRACYCLINE-INDUCED PLEURAL LOCULATION IN RABBITS (2007)

The authors compared the ability of a single dose of the proenzyme single-chain urokinase (scuPA), low-molecular-weight urokinase, tissue plasminogen activator (tPA), or a mutant site-inactive scuPA to resolve intrapleural loculations at 72 to 96 hours after tetracycline-induced pleural injury in rabbits. Both scuPA and tPA reversed loculations at 96 hours after injury P < or = .001, whereas low-molecular-weight urokinase and the scuPA mutant were ineffective. scuPA and tPA generated inhibitor complexes, induced fibrinolytic activity, and quenched plasminogen activator-1 activity in pleural fluids. The authors conclude that scuPA reverses loculations as effectively as tPA at clinically applied intrapleural doses, whereas low-molecular-weight urokinase was ineffective.
Changes in Cognitive Characteristics of Tg(APP)CRND8 Mice at Early Stages of Immunization with Beta‐Amyloid Peptide (2001)

The progressive cognitive dysfunction of Alzheimer's disease is accompanied by a series of neuropathological changes including parenchymal and blood vessel deposition of Beta-amyloid peptide in the human brain. Many lines of evidence indicate that abnormal processing of Beta-amyloid peptide (a proteolytic derivative of the Beta-amyloid precursor protein, βAPP) plays a central role in initiating the pathogenesis of Alzheimer's disease. There is also strong support for the positive correlation between Beta-amyloid plaques and cognitive impairment in Alzheimer's disease patients. However, there are gaps in our knowledge of the pathogenesis of even the ‘simple’ genetic forms of Alzheimer's disease. Thus there has been a need for animal models that develop some or all aspects of this uniquely human disease in a reproducible fashion to decipher and stratify crucial pathogenic events.
Dynamic Adjustment of Subtitles Using Audio Fingerprints (2015)

Anyone who ever downloaded subtitle files from the Internet has faced problems synchronizing them with the associated media files. Even with the efforts of communities on reviewing user-contributed subtitles and with mechanisms in movie players to automate the discovery of subtitles for a given media, users still face lip synchronization issues. In this work we conduct a study on several subtitle files associated with popular movies and TV series and analyze their differences. Based on that, we propose a two-phase subtitle synchronization method that annotates subtitles with audio fingerprints, which serve as synchronization anchors to the media player. Preliminary results obtained with our prototype suggest that our technique is effective and has minimal impact on the extension of subtitle formats and on media playback performance.
Water Confined in Lamellar Structures of AOT Surfactants: An Infrared Investigation (2002)

Both X-ray diffraction and infrared spectroscopy on water confined between the lamellar bilayers of aerosol-OT (AOT) allowed us to explore the differences in connectivity between bulk and confined water when water layer thicknesses are allowed to vary from 19.0 to 1.5 nm. Compared with previous studies on AOT reverse micelles, the present report in the lamellar mesophase allows one to cancel the micelle curvature contribution, which disrupts the water connectivity, too. The influence of AOT surface on the water connectivity degree was thus quantified alone in the mid infrared region (3000−3800 cm-1) in the OH stretching mode. The OH stretching mode peak can be fitted by three Gaussian peaks that describe three main connecting populations, namely the "multimer" water at c.a. 3585 cm-1, the "intermediary" water at c.a. 3465 cm-1, and the "network" water at c.a. 3320 cm-1. It is shown that interactions with the surfactant heads do not alter the water structure until the water layer shrinks below 4.0 nm and the hydration water molecules per surfactant are found to be equal to 2.6, in good agreement with equivalent studies on micellar systems.
Dietary restriction mitigates cocaine‐induced alterations of olfactory bulb cellular plasticity and gene expression, and behavior (2010)

Because the olfactory system plays a major role in food consumption, and because 'food addiction' and associated morbidities have reached epidemic proportions, we tested the hypothesis that dietary energy restriction can modify adverse effects of cocaine on behavior and olfactory cellular and molecular plasticity. Mice maintained on an alternate day fasting (ADF) diet exhibited increased baseline locomotion and increased cocaine-sensitized locomotion during cocaine conditioning, despite no change in cocaine conditioned place preference, compared with mice fed ad libitum. Levels of dopamine and its metabolites in the olfactory bulb (OB) were suppressed in mice on the ADF diet compared with mice on the control diet, independent of acute or chronic cocaine treatment. The expression of several enzymes involved in dopamine metabolism including tyrosine hydroxylase, monoamine oxidases A and B, and catechol-O-methyltransferase were significantly reduced in OBs of mice on the ADF diet. Both acute and chronic administration of cocaine suppressed the production of new OB cells, and this effect of cocaine was attenuated in mice on the ADF diet. Cocaine administration to mice on the control diet resulted in up-regulation of OB genes involved in mitochondrial energy metabolism, synaptic plasticity, cellular stress responses, and calcium- and cAMP-mediated signaling, whereas multiple olfactory receptor genes were down-regulated by cocaine treatment. ADF abolished many of the effects of cocaine on OB gene expression. Our findings reveal that dietary energy intake modifies the neural substrates underlying some of the behavioral and physiological responses to repeated cocaine treatment, and also suggest novel roles for the olfactory system in addiction. The data further suggest that modification of dietary energy intake could provide a novel potential approach to addiction treatments.
Data from Tumor-Associated MICA Is Shed by ADAM Proteases (2023)

&lt;div&gt;Abstract&lt;p&gt;The immunoreceptor NKG2D promotes immunosurveillance of malignant cells and protects the host from tumor initiation by activating natural killer cells and costimulating CD8 T cells. NKG2D-mediated recognition of malignant cells by cytotoxic lymphocytes is enabled through the tumor-associated expression of NKG2D ligands (NKG2DL) resulting from cellular or genotoxic stress. Shedding of NKG2DL is thought to constitute a major countermechanism of tumor cells to subvert NKG2D-mediated immunosurveillance. Here, we report that the prototypical NKG2DL MICA is released by proteolytic cleavage in the stalk of the MICA ectodomain, where deletions, but not alanine substitutions, impede MICA shedding. Small compound-mediated stimulation and inhibition of MICA shedding adduced characteristics that indicated an involvement of members of the “a disintegrin and metalloproteinase” (ADAM) family. Accordingly, MICA shedding by tumor cells was inhibited by silencing of the related ADAM10 and ADAM17 proteases, which are known to promote tumor growth by releasing epidermal growth factor receptor ligands. Collectively, our data show that ADAM10 and ADAM17 are critically involved in the tumor-associated proteolytic release of soluble MICA facilitating tumor immune escape. Hence, therapeutic blockade of ADAM10 and ADAM17 seems promising for cancer treatment by targeting both growth and immune escape of tumors. [Cancer Res 2008;68(15):6368–76]&lt;/p&gt;&lt;/div&gt;
<title>Novel design and fabrication of Si optical bench</title> (2001)

The insertion loss is highly affected by the optical path length for 2D or matrix type free space optical switch. Since the v-groove width of conventional Si optical bench is more than 25% larger than the diameter of lens, it is almost impossible to make the optical bench that has the smaller lens pitch than its diameter. In addition, owing to 'convex corner effect', the completed optical bench has the different etched pattern than expected which also makes it difficult to align the optical components. In this paper, novel design and fabrication of Si optical bench is proposed to solve these problems. We arranged the lenses meanderingly so the lens pitch could be shortened remarkably. New method to make perfect optical bench by wet etch and deep RIE process is also proposed. To compare the simulation result with the experimental one, we made the in-line type optical bench. Its maximum optical path is about 38 mm which is the same as that of the proposed 16x16 free space optical switch. From the optical simulation, the insertion loss is less than 2 dB and it agrees with the measured value within the experimental error.
Performance Evaluation of Barrier Techniques for Distributed Tracing Garbage Collector (2005)

Currently, software engineering is becoming even more complex due to distributed computing. In this new context, portability is one of the key issues and hence a cluster-aware Java Virtual Machine (JVM) that can transparently execute Java applications in a distributed fashion on nodes of a cluster, while providing the programmer with the single system image of a classical JVM, is really desirable. This way multi-threaded server applications can take advantage of cluster resources without increasing their programming complexity. However, such kind of JVM is not easy to design. Moreover, one of the most challenging tasks in its design is the development of an efficient, scalable and automatic dynamic memory manager. Inside this manager, one important module is the automatic recycling mechanism or garbage collector. This collector is a module with very intensive processing demands that must concurrently run with userâs application. It can consume a very significant portion of the total execution time spent inside JVM in uniprocessor systems, and its overhead increases in distributed garbage collection because of the update of changing references in different nodes. Hence, the garbage collector is a very critical part in distributed designs of JVMs, both for performance and energy. In this paper our contribution to automatic distributed garbage collection is two-fold. First, we have analyzed the barrier mechanism design space for the study of tracing-based distributed garbage collectors. Second, we have evaluated the impact of the most significative barrier strategies as main bottlenecks in global performance. Our preliminary results show that the choice of the specific technique used in barrier mechanisms produces significant differences both in performance and internodes messaging overhead.
Plasma Contains Ultra-short Single-stranded DNA in Addition to Nucleosomal cfDNA (2021)

ABSTRACT Plasma cell-free DNA is a widely used biomarker for diagnostic screening. We introduce uscfDNA-seq, a single-stranded cell-free DNA NGS pipeline, which bypasses previous limitations to reveal a novel population of ultrashort single-stranded cell-free DNA in plasma with a modal size of 50nt. This species of cfDNA aligns predominantly to the nuclear genome and could potentially be used for novel biomarker discovery.
Non-Nutritive Suckling System for Real-Time Characterization of Intraoral Vacuum Profile in Full Term Neonates (2022)

Infant breastfeeding diagnostics remain subjective due to the absence of instrumentation to objectively measure and understand infant oral motor skills and suckling characteristics. Qualitative diagnostic exams, such as the digital suck assessment which relies upon a clinician's gloved finger inserted into the infant's mouth, produce a diversity of diagnoses and intervention pathways due to their subjective nature. In this paper, we report on the design of a non-nutritive suckling (NNS) system which quantifies and analyzes quantitative intraoral vacuum and sucking patterns of full-term neonates in real time. In our study, we evaluate thirty neonate suckling profiles to demonstrate the technical and clinical feasibility of the system. We successfully extract the mean suck vacuum, maximum suck vacuum, frequency, burst duration, number of sucks per burst, number of sucks per minute, and number of bursts per minute. In addition, we highlight the discovery of three intraoral vacuum profile shapes that are found to be correlated to different levels of suckling characteristics. These results establish a framework for future studies to evaluate oromotor dysfunction that affect the appearance of these signals based on established normal profiles. Ultimately, with the ability to easily and quickly capture intraoral vacuum data, clinicians can more accurately perform suckling assessments to provide timely intervention and assist mothers and infants towards successful breastfeeding outcomes.
Hyperspectral Image Reconstruction from Multispectral Images Using Non-Local Filtering (2021)

Using light spectra is an essential element in many applications, for example, in material classification. Often this information is acquired by using a hyperspectral camera. Unfortunately, these cameras have some major disadvantages like not being able to record videos. Therefore, multispectral cameras with wide-band filters are used, which are much cheaper and are often able to capture videos. However, using multispectral cameras requires an additional reconstruction step to yield spectral information. Usually, this reconstruction step has to be done in the presence of imaging noise, which degrades the reconstructed spectra severely. Typically, same or similar pixels are found across the image with the advantage of having independent noise. In contrast to state-of-the-art spectral reconstruction methods which only exploit neighboring pixels by block-based processing, this paper introduces non-local filtering in spectral reconstruction. First, a block-matching procedure finds similar non-local multispectral blocks. Thereafter, the hyperspectral pixels are reconstructed by filtering the matched multispectral pixels collaboratively using a reconstruction Wiener filter. The proposed novel procedure even works under very strong noise. The method is able to lower the spectral angle up to 18% and increase the peak signal-to-noise-ratio up to 1.1dB in noisy scenarios compared to state-of-the-art methods. Moreover, the visual results are much more appealing.
<title>Advances on the fabrication of microchannel plate spatial light modulator based on LiNbO3 waveguide array</title> (1999)

Recently, we report a new type of micro channel plate spatial light modulator (MSLM), in which the bulk LiNbO<SUB>3</SUB> crystal plate is replaced by an electro-optic composite material, namely, single crystal waveguide array. This array is a 2D LiNbO<SUB>3</SUB> single crystal waveguide array, which consists of single crystal waveguides with filling materials among adjacent waveguides. Since the dielectric constant of LiNbO<SUB>3</SUB> single crystal is much higher than that of gap filling materials such as polymer/epoxy, the electric field can mostly be constrained inside the crystal material. In addition, by selecting proper opaque filling material, there are also no optical crosstalks among adjacent waveguides. Thus, this special waveguide array works as a 2D set of optically and electrically isolated light guides. While the sensitivity is unchanged, the spatial resolution can be increased. In this paper, a prototype of such a MSLM is presented. The manufacturing processes of the MSLM is introduced. The evaluation on the performance of the MSLM is also reported. The advantages and limitations of the MSLM are addressed.
Urban Mosaic: Visual Exploration of Streetscapes Using Large-Scale Image Data (2020)

Urban planning is increasingly data driven, yet the challenge of designing with data at a city scale and remaining sensitive to the impact at a human scale is as important today as it was for Jane Jacobs. We address this challenge with Urban Mosaic,a tool for exploring the urban fabric through a spatially and temporally dense data set of 7.7 million street-level images from New York City, captured over the period of a year. Working in collaboration with professional practitioners, we use Urban Mosaic to investigate questions of accessibility and mobility, and preservation and retrofitting. In doing so, we demonstrate how tools such as this might provide a bridge between the city and the street, by supporting activities such as visual comparison of geographically distant neighborhoods,and temporal analysis of unfolding urban development.
A hierarchical Bayesian approach for semi-supervised discriminative language modeling (2012)

Discriminative language modeling provides a mechanism for differentiating between competing word hypotheses, which are usually ignored in traditional maximum likelihood estimation of N-gram language models. Discriminative language modeling usually requires manual transcription which can be costly and slow to obtain. On the other hand, there are vast amount of untranscribed speech data on which offline adaptation technique can be applied to generate pseudo-truth transcription as an approximation to manual transcription. Viewing manual and pseudo-truth transcriptions as two domains, we perform domain adaptation on the discriminative language models via hierarchical Bayesian, in which the domainspecific models share a common prior model. Domainspecific and prior models are then estimated jointly using training data. On the N-best list rescoring experiment, hierarchical Bayesian has yielded better recognition performance than the model trained only on manual transcription, and is robust against inferior prior.
Fatigue Life Evaluation Technique for Multilayer Bellows Exhaust Pipe (2018)

In this study, we developed a fatigue life evaluation technique for multilayer bellows and got the following conclusions. (1) The fatigue life of the multilayer bellows is roughly in agreement with the fatigue life of the single layer bellows which can be evaluated with the best fit curve of stainless steel material. (2) The fatigue life of bellows should be evaluated taking into consideration that the fatigue life decreases due to the high-temperature atmosphere and the initial stress in the actual equipment mounting environment. (3) By deriving the relationship between the initial stress and the allowable stress using the stainless steel best fit curve, it is possible to evaluate the breakage of the bellows in the actual machine mounting environment.
ChemInform Abstract: TANTALUM‐NEOPENTYLIDENE HYDRIDE AND TANTALUM‐NEOPENTYLIDYNE HYDRIDE COMPLEXES (1981)

Abstract Die Reduktion des Ta‐neopentyl‐ Komplexes (Ia) mit Na‐Amalgam in Gegenwart von Trimethylphosphin liefert den Neopentyliden‐Komplex (IIa), analog reagiert der deuterierte Komplex (Ib) sowie der Komplex (III) zu (IV), der bei ‐30°C isoliert werden konnte.