gebhart/patrepeval huggingface dataset:
Marine Carotenoid Fucoxanthin Possesses Anti-Metastasis Activity: Molecular Evidence (2019)

Fucoxanthin is commonly found in marine organisms; however, to date, it has been one of the scarcely explored natural compounds. We investigated its activities in human cancer cell culture-based viability, migration, and molecular assays, and found that it possesses strong anticancer and anti-metastatic activities that work irrespective of the p53 status of cancer cells. In our experiments, fucoxanthin caused the transcriptional suppression of mortalin. Cell phenotype-driven molecular analyses on control and treated cells demonstrated that fucoxanthin caused a decrease in hallmark proteins associated with cell proliferation, survival, and the metastatic spread of cancer cells at doses that were relatively safe to the normal cells. The data suggested that the cancer therapy regimen may benefit from the recruitment of fucoxanthin; hence, it warrants further attention for basic mechanistic studies as well as drug development.
Design of Pyrrolic-N-Rich Carbon Dots with Absorption in the First Near-Infrared Window for Photothermal Therapy (2018)

Pyrrolic-N-rich carbon dots (CDs) that exhibit an absorption peak in the first near-infrared (NIR) window region were developed using a one-step microwave-assisted hydrothermal synthesis. A high concentration of urea enabled the introduction of a large amount of pyrrolic-nitrogen on the CD surfaces. Upon optimization of the experimental conditions, the absorption peak of the CDs red-shifted from 550 to 650 nm. The resulting pyrrolic-N-rich CDs exhibited photothermal effects with high NIR photothermal efficiency (54.3%) and photoluminescence. The prepared CDs, which show a first NIR window absorption peak, photoluminescence, and negative surface charge, have the potential to be used as multifunctional nanocarriers for cell imaging and drug delivery and as photothermal agents in cancer therapy.
A Generalized Linear Model for Estimating Spectrotemporal Receptive Fields from Responses to Natural Sounds (2011)

In the auditory system, the stimulus-response properties of single neurons are often described in terms of the spectrotemporal receptive field (STRF), a linear kernel relating the spectrogram of the sound stimulus to the instantaneous firing rate of the neuron. Several algorithms have been used to estimate STRFs from responses to natural stimuli; these algorithms differ in their functional models, cost functions, and regularization methods. Here, we characterize the stimulus-response function of auditory neurons using a generalized linear model (GLM). In this model, each cell's input is described by: 1) a stimulus filter (STRF); and 2) a post-spike filter, which captures dependencies on the neuron's spiking history. The output of the model is given by a series of spike trains rather than instantaneous firing rate, allowing the prediction of spike train responses to novel stimuli. We fit the model by maximum penalized likelihood to the spiking activity of zebra finch auditory midbrain neurons in response to conspecific vocalizations (songs) and modulation limited (ml) noise. We compare this model to normalized reverse correlation (NRC), the traditional method for STRF estimation, in terms of predictive power and the basic tuning properties of the estimated STRFs. We find that a GLM with a sparse prior predicts novel responses to both stimulus classes significantly better than NRC. Importantly, we find that STRFs from the two models derived from the same responses can differ substantially and that GLM STRFs are more consistent between stimulus classes than NRC STRFs. These results suggest that a GLM with a sparse prior provides a more accurate characterization of spectrotemporal tuning than does the NRC method when responses to complex sounds are studied in these neurons.
PUMA mediates the apoptotic response to p53 in colorectal cancer cells (2003)

Although several genes that might mediate p53-induced apoptosis have been proposed, none have previously been shown to play an essential role in this process through a rigorous gene disruption approach. We used a gene-targeting approach to evaluate p53-mediated death in human colorectal cancer cells. Expression of p53 in these cells induces growth arrest through transcriptional activation of the cyclin-dependent kinase inhibitor p21. If p21 is disrupted via gene targeting, the cells die through apoptosis. If the PUMA gene is also disrupted in such cells, apoptosis is prevented. The effects of PUMA on apoptosis were observed after exogenous overexpression of p53 as well as after exposure to hypoxia, a physiologic activator of p53, and DNA damage. The PUMA protein interacts with Bcl-X(L) and promotes mitochondrial translocation and multimerization of Bax. Accordingly, genetic disruption of BAX makes cells resistant to the apoptosis resulting from PUMA expression. These results suggest that the balance between PUMA and p21 is pivotal in determining the responses to p53 activation and provide a model for understanding the basis of p53 mutations in human cancer.
The interactions between antithrombin III, thrombin and surface immobilized heparin (1996)

The interactions between antithrombin III (ATIII), thrombin, and surface immobilized heparin were investigated. Carboxylated polystyrene modified with covalently immobilized albumin-heparin conjugate contain sites which can bind ATIII from buffer and plasma solutions. Approximately 65% of the ATIII molecules present at the heparinized surface either adsorbed from a buffer or plasma solution, exchanged with ATIII in buffer solution. The exchange between surface bound ATIII and ATIII in solution was repeated several times on the same heparinized surface. The number of binding sites that could bind and release ATIII was much higher when the heparinized surface was exposed to an ATIII containing buffer solution than to a plasma solution. The reduction in binding sites available for ATIII using plasma solutions as compared to buffer solutions could be explained by the competition of other plasma proteins with ATIII for the heparinized surface. It was observed that heparin binding proteins were able to compete with ATIII for binding to the immobilized heparin. Furthermore adsorption of proteins on the heparinized surface significantly reduced the availability of binding sites for ATIII. Exposure of thrombin to the heparinized surface resulted in thrombin activity at the surface. The thrombin activity on the heparinized surfaces was lower on surfaces with a higher ATIII concentration. The activity of surface bound thrombin was not affected by the presence of other plasma proteins. Enzymatically active thrombin molecules present at the heparinized surface were completely inactivated when the surface was exposed to a solution containing ATIII. The inactivation rate of surface bound thrombin by ATIII was higher than the rate of the uncatalyzed inactivation of thrombin in solution. Part of the Thrombin-Antithrombin III (TAT) complexes (10-20%) that were formed upon inactivation of thrombin remained bound to the heparinized surface. In general it was concluded that only the surface immobilized heparin molecules that can bind ATIII in a reversible way determine the anticoagulant properties of the surface. The mechanism of inactivation of a protease on a heparinized surface depends either on the catalytic effect of heparin on the inactivation rate of proteases by ATIII or on an increased uncatalytic inactivation due to increased concentrations of ATIII near the surface as compared to the concentration of ATIII in the bulk phase.
Thin-film heterojunction field-effect transistors for ultimate voltage scaling and low-temperature large-area fabrication of active-matrix backplanes (2014)

Thin-Film heterojunction field-effect transistor (HJFET) devices with crystalline Si (c-Si) channels and gate regions comprised of hydrogenated amorphous silicon (a-Si:H) or organic materials are demonstrated. The HJFET devices are processed at 200°C and room temperature, respectively; and exhibit operation voltages below 1V, subthreshold slopes in the range of 70-100mV/dec and off-currents as low as 25 fA/μm. The HJFET devices are proposed for use in active matrix backplanes comprised of low-temperature poly-Si (LTPS) as the c-Si substrate. Compared to conventional LTPS devices which require process temperatures up to 600°C and complex fabrication steps, the HJFET devices offer lower process temperature, simpler fabrication steps and lower operation voltages without compromising leakage or stability.
Bacterial phenotype identification using Zernike moment invariants (2006)

Pathogenic bacterial contamination in food products is costly to the public and to industry. Traditional methods for detection and identification of major food-borne pathogens such as <i>Listeria monocytogenes</i> typically take 3-7 days. Herein, the use of optical scattering for rapid detection, characterization, and identification of bacteria is proposed. Scatter patterns produced by the colonies are recognized without the need to use any specific model of light scattering on biological material. A classification system was developed to characterize and identify the scatter patterns obtained from colonies of various species of <i>Listeria</i>. The proposed classification algorithm is based on Zernike moment invariants (features) calculated from the scatter images. It has also been demonstrated that even a simplest approach to multivariate analysis utilizing principal component analysis paired with clustering or linear discriminant analysis can be successfully used to discriminate and classify feature vectors computed from the bacterial scatter patterns.
Development of fiber-optic current sensing technique and its applications in electric power systems (2013)

This paper describes the development and applications of a fiber-optic electric current sensing technique with the stable properties and compact, simple, and flexible structure of the sensing device. The special characteristics of the sensors were achieved by use of the special low birefringence fiber as the Faraday-effect sensing element and were also achieved with creation of sensing schemes which matched with the features of the fiber. Making use of the excellent features of the sensing technique, various current monitoring devices and systems were developed and applied practically for the control and maintenance in the electric power facility. In this paper, the design and performance of the sensing devices are introduced first. After that, examples of the application systems practically applied are also introduced, including fault section/point location systems for power transmission cable lines.
Self-aligned double patterning decomposition for overlay minimization and hot spot detection (2011)

Self-aligned double patterning (SADP) lithography is a promising technology which can reduce the overlay and print 2D features for sub-32nm process. Yet, how to decompose a layout to minimize the overlay and perform hot spot detection is still an open problem. In this paper, we present an algorithm that can optimally solve the SADP decomposition problem. For a decomposable layout, our algorithm guarantees to find a decomposition solution that minimizes overlay. For a non-decomposable layout our algorithm guarantees to find all hot spots. Experimental results validate our method, and decomposition results for Nangate Open Cell Library and larger testcases are also provided with competitive runtimes.
Mobility support in qos signaling of multiple path sessions (2006)

Ubiquitous access and content rich service are the focus of next generation networking. With the advancement in access technologies, dual or even multiple access devices are widely adopted to achieve the anytime-anywhere connection. However, the connection itself does not guarantee a smooth service to the user. Mobility and Quality-of-Service (QoS) control are the key points to deliver services with seamless and transparent transitions. Compared to the enormous number of mobility solutions proposed to that end, corresponding QoS signaling support is lagging behind. This article presents some considerations for the QoS signaling for the multiple flow and path sessions. It is revealed that current signaling schemes have no proper support of such cases. In view of this, a solution is proposed as remedy followed by detail operation analysis. Requiring only minor amendments to a current scheme, the solution provides an extensible way to realize QoS control for multi-flow and/or multi-path sessions.
A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs (2010)

Chromatin immunoprecipitation (ChIP) followed by high throughput sequencing (ChIP-seq) is rapidly becoming the method of choice for discovering cell-specific transcription factor binding locations genome wide. By aligning sequenced tags to the genome, binding locations appear as peaks in the tag profile. Several programs have been designed to identify such peaks, but program evaluation has been difficult due to the lack of benchmark data sets. We have created benchmark data sets for three transcription factors by manually evaluating a selection of potential binding regions that cover typical variation in peak size and appearance. Performance of five programs on this benchmark showed, first, that external control or background data was essential to limit the number of false positive peaks from the programs. However, >80% of these peaks could be manually filtered out by visual inspection alone, without using additional background data, showing that peak shape information is not fully exploited in the evaluated programs. Second, none of the programs returned peak-regions that corresponded to the actual resolution in ChIP-seq data. Our results showed that ChIP-seq peaks should be narrowed down to 100-400 bp, which is sufficient to identify unique peaks and binding sites. Based on these results, we propose a meta-approach that gives improved peak definitions.
Addressing overdiagnosis and overtreatment in cancer: a prescription for change (2020)

A vast range of disorders—from indolent to fast-growing lesions—are labelled as cancer. Therefore, we believe that several changes should be made to the approach to cancer screening and care, such as use of new terminology for indolent and precancerous disorders. We propose the term indolent lesion of epithelial origin, or IDLE, for those lesions (currently labelled as cancers) and their precursors that are unlikely to cause harm if they are left untreated. Furthermore, precursors of cancer or high-risk disorders should not have the term cancer in them. The rationale for this change in approach is that indolent lesions with low malignant potential are common, and screening brings indolent lesions and their precursors to clinical attention, which leads to overdiagnosis and, if unrecognised, possible overtreatment. To minimise that potential, new strategies should be adopted to better define and manage IDLEs. Screening guidelines should be revised to lower the chance of detection of minimal-risk IDLEs and inconsequential cancers with the same energy traditionally used to increase the sensitivity of screening tests. Changing the terminology for some of the lesions currently referred to as cancer will allow physicians to shift medicolegal notions and perceived risk to reflect the evolving understanding of biology, be more judicious about when a biopsy should be done, and organise studies and registries that offer observation or less invasive approaches for indolent disease. Emphasis on avoidance of harm while assuring benefit will improve screening and treatment of patients and will be equally effective in the prevention of death from cancer.
Palm vein authentication technology and its applications (2005)

This paper discusses the contactless palm vein authentication device that uses blood vessel patterns as a personal identifying factor. The vein information is hard to duplicate since veins are internal to the human body. The palm vein authentication technology offers a high level of accuracy, and delivers the following results: a false rejection rate (FRR) of 0.01%, and a false acceptance rate (FAR) of 0.00008% or lower, based on Fujitsu research using the data of 140,000 palms. Several banks in Japan have used the palm vein authentication technology for customer identification since July 2004. In addition, Fujitsu has integrated the technology into the access control of electronic door lock systems. Fujitsu plans to further expand applications for this technology by downsizing the sensor and improving the verification speed. 1. Palm vein authentication Palm vein authentication uses the vascular patterns of an individual’s palm as personal identification data. Compared with a finger [1] or the back of a hand, a palm has a broader and more complicated vascular pattern and thus contains a wealth of differentiating features for personal identification. The palm is an ideal part of the body for this technology; it normally does not have hair which can be an obstacle for photographing the blood vessel pattern, and it is less susceptible to a change in skin color, unlike a finger or the back of a hand. The deoxidized hemoglobin in the vein vessels absorb light having a wavelength of about 7.6 x 10 -4 mm within the near-infrared area [2]. When the infrared ray image is captured, unlike the image seen in Fig.1, only the blood vessel pattern containing the deoxidized hemoglobin is visible as a series of dark lines (Fig.2). Based on this feature, the vein authentication device translates the black lines of the infrared ray image as the blood vessel pattern of the palm (Fig. 3), and then matches it with the previously registered blood vessel pattern of the individual. 2. Implementation of contactless palm vein authentication The contactless palm vein authentication technology consists of image sensing and software technology. The palm vein sensor (Fig.4) captures an infrared ray image of the user’s palm. The lighting of the infrared ray is controlled depending on the illumination around the sensor, and the sensor is able to capture the palm image regardless of the position and movement of the palm. The software then matches the translated vein pattern with the registered pattern, while measuring the position and orientation of the palm by a pattern matching method.
Luminescence of Sn^2+ center in oxide glass with a tendency toward phase separation (2017)

Photoluminescence (PL) of Sn2+ in oxide glasses is affected by the local coordination field because of the electrons in the outermost shell. Not only the emission energy varies depending on the local coordination, but also the transparency, and it is worth examining the local distribution of Sn2+ cations in oxide glasses, which have a tendency toward phase separation, especially in an ionic (phosphate)–covalent (borate) binary system. Here, we report the structural changes in zinc borophosphate glass and the PL properties of Sn2+ in oxide glasses. The building blocks of the main glass network vary depending on the chemical composition. We found that the Sn2+ species in B2O3-rich glasses differ from those in P2O5-rich glasses, as observed in the optical absorption, PL peaks, and PL decay constants. 119Sn Mossbauer spectra indicate that isomer shifts of Sn2+ also affect the local coordination change depending on the chemical composition. According to these results for the Sn2+ center, we conclude that Sn2+ centers are homogeneously dispersed in the borophosphate network without localization around the phosphate region.
Effect of Charge Non-uniformity on Heat Release and Emissions in PCCI Engine Combustion (2006)

&lt;div class="htmlview paragraph"&gt;Homogeneous Charge Compression Ignition (HCCI) engines are currently of great interest as a future alternative to Diesel and Spark Ignition engines because of HCCI's potential to achieve high efficiency with very low NO&lt;sub&gt;x&lt;/sub&gt; emissions. However, significant technical barriers remain to practical implementation of HCCI engines: difficult-to-control combustion, low power density, rapid pressure rise, and high hydrocarbon and carbon monoxide emissions. To overcome some of these barriers, operational strategies that involve relaxing the constraint of truly “homogeneous” HCCI combustion have been studied. The phrase “Premixed Charge Compression Ignition” or “PCCI” combustion can be used to describe this class of combustion processes, in which combustion occurs similarly to HCCI engines as a non-mixing controlled, chemical kinetics dominated, auto-ignition process, but the fuel, air, and residual gas mixture need not be homogeneous.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;This paper presents analysis of the effect of charge non-uniformity upon combustion in PCCI engines. The analysis is conducted using a numerical approach for simulation of PCCI that utilizes a fully-coupled combination of multi-dimensional computational fluid mechanics with a multi-zone detailed chemical kinetics solver. Baseline simulations have been validated against HCCI experiments with isooctane fuel. Further simulations have been conducted to assess the effect of charge non-uniformity on the heat release and emissions for PCCI operation. The results show that charge non-uniformity used in the PCCI strategy may sometimes have a beneficial effect of reducing carbon monoxide and hydrocarbon emissions. However, charge non-uniformity within the combustion chamber has the potential to increase NO&lt;sub&gt;x&lt;/sub&gt; emissions.&lt;/div&gt;
Stable Molybdenum Oxide Cathodes: Achieving Stable Molybdenum Oxide Cathodes for Aqueous Zinc‐Ion Batteries in Water‐in‐Salt Electrolyte (Adv. Mater. Interfaces 9/2021) (2021)

In article number 2002080, Lei Wang, Amy C. Marschilok, and co-workers report that a zinc chloride water-in-salt electrolyte is utilized for the first time to significantly increase the stability of an aqueous zinc/molybdenum oxide battery by forming a special surface layer protecting the zinc anode surface from dissolved molybdenum species and hydrogen gas evolution.
Figure S4 from JAK1/STAT3 Activation through a Proinflammatory Cytokine Pathway Leads to Resistance to Molecularly Targeted Therapy in Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Figure S4. rhOSM treatment resulted in EMT-associated changes in NSCLC cells. H23 cells treated or not treated (Mock) with rhOSM (10 ng/mL) for 1 week were subjected to phase-contrast imaging. rhOSM treatment caused morphological change to a spindle shape.&lt;/p&gt;
The Physiology of Homeoprotein Transduction (2018)

The homeoprotein family comprises ~300 transcription factors and was long seen as primarily involved in developmental programs through cell autonomous regulation. However, recent evidence reveals that many of these factors are also expressed in the adult where they exert physiological functions not yet fully deciphered. Furthermore, the DNA-binding domain of most homeoproteins contains two signal sequences allowing their secretion and internalization, thus intercellular transfer. This review focuses on this new-found signaling in cell migration, axon guidance, and cerebral cortex physiological homeostasis and speculates on how it may play important roles in early arealization of the neuroepithelium. It also describes the use of homeoproteins as therapeutic proteins in mouse models of diseases affecting the central nervous system, in particular Parkinson disease and glaucoma.