gebhart/patrepeval huggingface dataset:
Amyloid clearance defect in ApoE4 astrocytes is reversed by epigenetic correction of endosomal pH (2018)

Endosomes have emerged as a central hub and pathogenic driver of Alzheimer's disease (AD). The earliest brain cytopathology in neurodegeneration, occurring decades before amyloid plaques and cognitive decline, is an expansion in the size and number of endosomal compartments. The strongest genetic risk factor for sporadic AD is the ε4 allele of Apolipoprotein E (ApoE4). Previous studies have shown that ApoE4 potentiates presymptomatic endosomal dysfunction and defective endocytic clearance of amyloid beta (Aβ), although how these two pathways are linked at a cellular and mechanistic level has been unclear. Here, we show that aberrant endosomal acidification in ApoE4 astrocytes traps the low-density lipoprotein receptor-related protein (LRP1) within intracellular compartments, leading to loss of surface expression and Aβ clearance. Pathological endosome acidification is caused by ε4 risk allele-selective down-regulation of the Na<sup>+</sup>/H<sup>+</sup> exchanger isoform NHE6, which functions as a critical leak pathway for endosomal protons. In vivo, the NHE6 knockout (NHE6<sup>KO</sup>) mouse model showed elevated Aβ in the brain, consistent with a causal effect. Increased nuclear translocation of histone deacetylase 4 (HDAC4) in ApoE4 astrocytes, compared with the nonpathogenic ApoE3 allele, suggested a mechanistic basis for transcriptional down-regulation of NHE6. HDAC inhibitors that restored NHE6 expression normalized ApoE4-specific defects in endosomal pH, LRP1 trafficking, and amyloid clearance. Thus, NHE6 is a downstream effector of ApoE4 and emerges as a promising therapeutic target in AD. These observations have prognostic implications for patients who have Christianson syndrome with loss of function mutations in NHE6 and exhibit prominent glial pathology and progressive hallmarks of neurodegeneration.
Esophageal carcinoma: pretherapy staging by computed tomography (1981)

Fifty-two patients with proven esophageal malignancy underwent esophagography, computed tomography (CT). esophagoscopy, and/or surgical exploration and resection. On the basis of CT findings, esophageal carcinoma was classified into four stages: stage I, intraluminal mass without esophageal wall thickening; stage II, esophageal wall thickening (greater than 5 mm); stage III, esophageal wall thickening and contiguous spread of tumor into adjacent mediastinal structures such as the trachea, bronchi, aorta, or atrium; and stage IV, any stage with evidence of distant metastatic disease. The stage of esophageal malignancy as determined by CT was correlated with symptoms, location of tumor, esophagography, and surgical findings. Results indicated that CT staging of esophageal carcinoma correlated closely with surgical findings and that local extension, regional adenopathy, and size of tumor mass were better evaluated by computed tomography than by other methods. CT is an accurate method of preoperatively staging esophageal carcinoma, capable of providing staging information heretofore only available by surgical exploration.
Development of a Novel Centrifugal Pump: Magnetic Rotary Pump (1997)

The rotational axis of the centrifugal pump has some associated problems such as blood destruction and sealing between the axis and pump housing. To improve upon these deficits we have developed a new type of blood pump, the magnetic rotary pump (MRP). The MRP has an original design with no rotational axis and no impellers. We made a prototype MRP and examined its hemodynamics in mock circulation. The prototype MRP flow rate is only 1.0 L/min with an afterload of 30 mm Hg, and we have made some modifications in the size and drive mechanisms from these results. The modified MRP can achieve high flow rates and rotational speeds (6.0 L/min with an afterload of 100 mm Hg, 2,000 rpm) in a mock circuit, and the modified MRP was used for left heart assistance in an acute animal experiment. The MRP could maintain the hemodynamics of an anesthetized adult goat. These results suggest that the MRP needs to be improved in several areas, but the MRP may be useful as a blood pump.
Recognition of traffic signs by artificial neural network (2002)

An artificial neural network system for traffic sign recognition is proposed in the paper. The input image is first processed for extraction of color and geometric information. A morphological filter is applied to increase the saliency by eliminating smaller objects and by linking together objects broken in disjoint parts due to noise. The coordinates of the resulting objects are determined, and the objects are isolated from the original image according to these coordinates. After this, the objects are normalized and sent to the neural network which performs the recognition. The neural network consists of classification subnetwork, winner-takes-all subnetwork (Hopfield network), and validation subnetwork. By introducing the new concept of a validation sub-network, the network enhance the capability to correctly classify the different traffic signs and avoid misclassifying nontraffic signs into a traffic sign. The system is tested by simulation as a whole and in part on a large amount of data acquired by a video camera attached to a vehicle frame by frame. The performance is encouraging. It produced excellent results except for the images under very poor illumination such that the color threshold (preprocessing) fails to extract the color information.
Study of Different Deep Learning Approach with Explainable AI for Screening Patients with COVID-19 Symptoms: Using CT Scan and Chest X-ray Image Dataset (2020)

The outbreak of COVID-19 disease caused more than 100,000 deaths so far in the USA alone. It is necessary to conduct an initial screening of patients with the symptoms of COVID-19 disease to control the spread of the disease. However, it is becoming laborious to conduct the tests with the available testing kits due to the growing number of patients. Some studies proposed CT scan or chest X-ray images as an alternative solution. Therefore, it is essential to use every available resource, instead of either a CT scan or chest X-ray to conduct a large number of tests simultaneously. As a result, this study aims to develop a deep learning-based model that can detect COVID-19 patients with better accuracy both on CT scan and chest X-ray image dataset. In this work, eight different deep learning approaches such as VGG16, InceptionResNetV2, ResNet50, DenseNet201, VGG19, MobilenetV2, NasNetMobile, and ResNet15V2 have been tested on two dataset-one dataset includes 400 CT scan images, and another dataset includes 400 chest X-ray images studied. Besides, Local Interpretable Model-agnostic Explanations (LIME) is used to explain the model's interpretability. Using LIME, test results demonstrate that it is conceivable to interpret top features that should have worked to build a trust AI framework to distinguish between patients with COVID-19 symptoms with other patients.
Optimal polarizations for partially polarized backscatter (1985)

Optimal polarizations are those which produce nulls in the co-polarized (CO-POL) and cross-polarized (X-POL) components of backscattered radiation. The discussion of optimal polarizations is here extended to the partially polarized case where nulls are replaced by minima. The width of the minima is related to the degree of polarization of the received radiation and, experimentally, to the correlation of orthogonal components. Formulas are presented for the location and width of these minima.
Inhibition of human tumor growth by intraperitoneal immunotoxins in nude mice. (1990)

Intracavitary administration of immunotoxins may play a role in the control of malignant effusions. Selection of immunotoxins for this form of therapy is based on their prior evaluation in preclinical studies. Monoclonal antibodies (mAb) 454A12 (antitransferrin receptor), and 260F9 are directed against antigens which are present on tumor cells in pleural and peritoneal effusions of patients with adenocarcinoma of the breast and ovary. In the present study, immunotoxins derived by conjugating these mAb to recombinant ricin A (rRA) were shown to be cytotoxic to human ovarian adenocarcinoma HEY cells in vitro and in vivo. In the in vitro assay 454A12-rRA and 260F9-rRA were 1000-fold and 10-fold, respectively, more cytotoxic than free rRa against HEY cells, and both immunotoxins were potentiated approximately 1000-fold by monensin. For in vivo studies HEY cells were injected i.p. into nude mice at a challenge dose (3 x 10(5) cells) which produced carcinomatosis with ascites, leading to death 30 days following injection. Administration of 454A12-rRA i.p. following the challenge dose resulted in a complete cure, whereas administration of 260 F9-rRA with monensin significantly prolonged survival. The greater cytotoxicity of 454A12-rRA than 260F9-rRA against HEY cells could be accounted for by the greater number of binding sites and higher internalization rate for 454A12-rRA and mAb 454A12 than 260F9-rRA and mAb 260F9, respectively. These results suggest a potential role for 454A12-rRA and 260F9-rRA plus monensin in the intracavitary therapy of malignant effusions associated with carcinoma of breast and ovary. In the case of 260F9-rRA, this represents the first preliminary indication of the suitability of this immunotoxin for intracavitary therapy of malignancies.
Mechanisms associated with biogenesis of exosomes in cancer (2019)

Intercellular communication between cellular compartments within the tumor and at distant sites is critical for the development and progression of cancer. Exosomes have emerged as potential regulators of intracellular communication in cancer. Exosomes are nanovesicles released by cells that contain biomolecules and are exchanged between cells. Exchange of exosomes between cells has been implicated in a number of processes critical for tumor progression and consequently altering exosome release is an attractive therapeutic target. Here, we review current understanding as well as gaps in knowledge regarding regulators of exosome release in cancer.
Self-reproduction for articulated behaviors with dual humanoid robots using on-line decision tree classification (2011)

SUMMARY We have proposed a new repetition framework for vision-based behavior imitation by a sequence of multiple humanoid robots, introducing an on-line method for delimiting a time-varying context. This novel approach investigates the ability of a robot “student” to observe and imitate a behavior from a “teacher” robot; the student later changes roles to become the “teacher” for a naïve robot. For the many robots that already use video acquisition systems for their real-world tasks, this method eliminates the need for additional communication capabilities and complicated interfaces. This can reduce human intervention requirements and thus enhance the robots' practical usefulness outside the laboratory. Articulated motions are modeled in a three-layer method and registered as learned behaviors using color-based landmarks. Behaviors were identified on-line after each iteration by inducing a decision tree from the visually acquired data. Error accumulated over time, creating a context drift for behavior identification. In addition, identification and transmission of behaviors can occur between robots with differing, dynamically changing configurations. ITI, an on-line decision tree inducer in the C4.5 family, performed well for data that were similar in time and configuration to the training data but the greedily chosen attributes were not optimized for resistance to accumulating error or configuration changes. Our novel algorithm, OLDEX identified context changes on-line, as well as the amount of drift that could be tolerated before compensation was required. OLDEX can thus identify time and configuration contexts for the behavior data. This improved on previous methods, which either separated contexts off-line, or could not separate the slowly time-varying context into distinct regions at all. The results demonstrated the feasibility, usefulness, and potential of our unique idea for behavioral repetition and a propagating learning scheme.
A Second Generation Formal Synthesis of (−)-Cephalotaxine (2008)

A second generation formal synthesis of the alkaloid (-)-cephalotaxine has been achieved using an alkylidene carbene 1,5-CH insertion reaction to establish a key quaternary stereocenter. The carbene precursor was readily derived from L-proline, and the 1,5-CH insertion reaction was performed under Ohira's conditions using lithiotrimethylsilyldiazomethane (LTDM), which gave the desired spirocyclic product in 74% yield. The hydroxymethyl group was then oxidized and then decarbonylated (93%), and this material was easily transformed into the desired Friedel-Crafts cyclization precursor. Exposure of this material to SnCl4 then gave the desired pentacyclic product, which was identical to that previously prepared by Mori and thus represents a formal total synthesis of (-)-cephalotaxine.
Direct blockade of antigen-reactive B lymphocytes by immune complexes. An 'off' signal for precursors of IgM-producing cells provided by the linkage of antigen-and Fc-receptors. (1978)

Antigen-antibody complexes efficiently inhibit the induction of antibody formation. Using Mishell-Dutton cultures, it can be demonstrated that neither T cells nor their products are required for this inhibition of IgM PFC formation. The blockade is at the level of B cells and cannot be overcome by LPS or TRF. The data demonstrate that cross-linking of antigen- and Fc-receptors by antigen-antibody complexes is a blocking signal for B cells.
Synergistic antitumor effects of CpG oligodeoxynucleotide and STAT3 inhibitory agent JSI‐124 in a mouse melanoma tumor model (2008)

One of the major limitations for cancer immunotherapy is related to the frequent existence of an intra‐tumoral immunosuppressive environment, to which STAT3 (Signal transducer and activator of transcription‐3) activation in tumor and dendritic cells (DCs) are believed to contribute. In this study, we tested the hypothesis that the combination of CpG (a DC activator) and JSI‐124 (a STAT3 inhibitor) may generate synergistic antitumor effects compared to CpG or JSI‐124 alone. B16‐F10, a mouse melanoma cell line that has constitutively active STAT3, was grafted in C57BL/6 mice and then tumor‐bearing mice treated intra‐tumorally with (a) phosphate buffered saline, (b) 10 μg CpG, (c) 1 mg kg −1 JSI‐124 or (d) 10 μg CpG+1 mg kg −1 JSI‐124. The effects of treatments on tumor growth, survival and antitumor immune responses were evaluated. Although significant antitumor effects were detected with the single‐agent treatments, the CpG+JSI‐124 treatment resulted in synergistic antitumor effects compared to CpG or JSI‐124 alone. Correlating with these findings, the combination therapy resulted in significantly higher intra‐tumoral levels of several proinflammatory, T H 1‐related cytokines (including IL‐12, IFN‐γ, TNF‐α and IL‐2), increases in intra‐tumoral CD8 + and CD4 + T cells expressing activation/memory markers and NK cells and increases in activated DCs in the tumors and regional lymph nodes (LNs). Concomitantly, the combination therapy led to a significantly decreased level of immunosuppression, as evidenced by lower intra‐tumoral level of VEGF and TGF‐β, and decreased number of CD4 + CD25 + Foxp3 + regulatory T cells in the regional LNs. This study has provided the proof‐of‐principle for combining CpG and JSI‐124 to enhance antitumor immune responses.
Analysis of breath volatile organic compounds as a noninvasive tool to diagnose nonalcoholic fatty liver disease in children (2013)

Exhaled breath analysis is a promising noninvasive method to detect fatty liver in children. Isoprene, acetone, trimethylamine, acetaldehyde, and pentane are novel biomarkers that may help to gain insight into pathophysiological processes leading to the development of NAFLD.
THz imaging with low-cost 130 nm CMOS transistors (2010)

We report on active imaging with CMOS transistors at 300 GHz and 1.05 THz. Two basic focal plane arrays consisting of nMOS transistors and wide-band bow-tie antennas have been implemented in a low-cost 130 nm CMOS technology. Raster scan imaging of objects concealed in a paper envelope has been achieved at 300 GHz with a commercial radiation source. The images clearly reveal the concealed objects with a dynamic range of 35 dB and a resolution of 3 mm. At 1.05 THz, the pixels achieve a responsivity of 50 V/W and a noise equivalent power of 900 pW/Hz<sup>0.5</sup>.
Irinotecan Delivery by Microbubble-Assisted Ultrasound: <i>In Vitro</i> Validation and a Pilot Preclinical Study (2013)

Irinotecan is a powerful anticancer drug with severe systemic side effects that limit its clinical application. Drug-targeted delivery with noninvasive methods is required to enhance the drug concentration locally and to reduce these undesirable events. Microbubble-assisted ultrasound has become a promising method for noninvasive targeted drug delivery. The aim of this study is to evaluate the therapeutic effectiveness of in vitro and in vivo irinotecan delivery based on the combination of ultrasound and microbubbles. In the present study, in vitro results showed that the irinotecan treatment with microbubble-assisted ultrasound induced a significant decrease in cell viability of human glioblastoma cells. Moreover, using subcutaneous glioblastoma xenografts, the in vivo preclinical study in nude mice demonstrated that this therapeutic protocol led to a decrease in tumor growth and perfusion and an increase of tumor necrosis. The conclusions drawn from this study demonstrate the promising potential of this therapeutic approach for the anticancer targeted therapy.
Multiple <i>Didymella</i> teleomorphs are linked to the <i>Phoma clematidina</i> morphotype (2009)

The fungal pathogen Phoma clematidina is used as a biological agent to control the invasive plant species Clematis vitalba in New Zealand. Research conducted on P. clematidina as a potential biocontrol agent against C. vitalba, led to the discovery of two perithecial-forming strains. To assess the diversity of P. clematidina and to clarify the teleomorph-anamorph relationship, phylogenetic analyses of 18 P. clematidina strains, reference strains representing the Phoma sections in the Didymellaceae and strains of related species associated with Clematis were conducted. Partial sequences of the ITS1, ITS2 and 5.8S rRNA gene, the ss-tubulin gene and 28S rRNA gene were used to clarify intra- and inter-species relationships. These analyses revealed that P. clematidina resolves into three well-supported clades which appear to be linked to differences in host specificity. Based on these findings, Didymella clematidis is newly described and the descriptions of P. clematidina and D. vitalbina are amended.
Demonstration of Spectral Defragmentation in Flexible Bandwidth Optical Networking by FWM (2011)

Flexible bandwidth elastic optical networking is an attractive solution for efficiently matching allocated bandwidth with link demand, but suffers from inevitable spectral fragmentation. In this letter, we discuss spectral defragmentation in flexible bandwidth networks using four-wave mixing (FWM) and wavelength selective switch (WSS)-based wavelength conversion blocks. Simulations show a defragmentation degree of one (i.e., the number of defragmentation blocks equals one) results in 71% and 47% reductions in blocking probability under high offered load (680 Erlangs) and low offered load (220 Erlangs), respectively. Further reductions in blocking probability result from an increased defragmentation degree. Experimental results show spectral defragmentation over 500 GHz of bandwidth for a defragmentation degree of one, validating FWM- and WSS-based spectral defragmentation in flexible bandwidth networks.
Near-Field Scanning Nanophotonic Microscopy—Breaking the Diffraction Limit Using Integrated Nano Light-Emitting Probe Tip (2009)

We introduce a novel scanning ldquonanophotonicrdquo microscope through monolithic integration of a nanoscale LED (Nano-LED) on a silicon cantilever. We review two recent trends of incorporating miniature light sources on the scanning probes for near-field scanning optical microscopy: one is to attach fluorephores at the tip to define a small light source, while the other is to integrate an LED and a nanometer aperture into scanning probes, based on silicon microfabrication techniques. The creation of Nano-LED combines the advantages of previous two approaches: no external sources are required and the reduction of the light source size directly leads to resolution improvement. Two types of Nano-LEDs have been successfully demonstrated utilizing nanofabrication and microelectromechanical systems technologies: 1) formation of thin silicon dioxide light-emitting layer between heavily doped p + and n+ silicon layers created by a focused ion beam and 2) electrostatic trapping and excitation of CdSe/ZnS core-shell nanoparticles in a nanogap. We employed these probes into a standard near-field scanning and excitation setup. The probe successfully measured optical as well as topographic images of chromium test patterns with imaging resolutions of 400 and 50 nm, respectively. In addition, the directional resolution dependence of the acquired images suggests the size and shape of the light source. To our knowledge, these results are probably the first successful near-field images directly measured by such tip-embedded light sources. With the potential emission capability from near UV to IR and additional mass producibility, the nanophotonic microscope presents exciting opportunities in near-field optics, integrated circuit technology, nanomanufacturing and molecular imaging, and sensing in biomedicine.
Building a lightweight eyetracking headgear (2004)

Eyetracking systems that use video-based cameras to monitor the eye and scene can be made significantly smaller thanks to tiny micro-lens video cameras. Pupil detection algorithms are generally implemented in hardware, allowing for real-time eyetracking. However, it is likely that real-time eyetracking will soon be fully accomplished in software alone. This paper encourages an "open-source" approach to eyetracking by providing practical tips on building a lightweight eyetracker from commercially available micro-lens cameras and other parts. While the headgear described here can be used with any dark-pupil eyetracking controller, it also opens the door to open-source software solutions that could be developed by the eyetracking and image-processing communities. Such systems could be optimized without concern for real-time performance because the systems could be run offline.