gebhart/patrepeval huggingface dataset:
Expression of the angiopoietins and their receptor Tie2 in human renal clear cell carcinomas; regulation by the von Hippel‐Lindau gene and hypoxia (2002)

Angiogenesis is essential for tumour growth and metastasis, and is co-ordinated by several classes of angiogenic factors. To determine the significance and regulation of the angiopoietin (Ang) pathway in highly vascular human renal cell carcinomas (RCCs), this study has investigated the expression of the Ang-1, Ang-2, Ang-4, and Tie2 genes in a series of normal (n = 26) and neoplastic (n = 45; clear cell n = 35, papillary n = 10) human kidney tissues, examined the pattern of Ang-2 and Tie2 protein expression, and correlated expression with clinicopathological variables. The effect of the von Hippel-Lindau (VHL) gene and hypoxia in the renal cell lines RCC786-0 and RCC4 has also been investigated. Ang-1, Ang-2 and Tie2, but not Ang-4 mRNA, were detected in normal and tumour samples. A significant increase in Ang-2 (p < 0.001) and a decrease in Tie2 receptor mRNA (p = 0.001) were observed, but no significant difference was observed in Ang-1 mRNA abundance between normal kidney and RCC (p = 0.37). Immunohistochemistry for Ang-2 showed strong expression in vascular endothelium and weak expression in tumour cells, whereas Tie2 was expressed exclusively on endothelium. Tie2 gene expression was positively correlated with Ang-2 expression in cancers (p = 0.001) and showed a borderline significant association with Ang-1 (p = 0.06), but there was no significant relationship between Ang-1 and Ang-2 (p = 0.69). No significant relationships were observed in clear cell carcinomas between Ang-1, Ang-2 and Tie2 mRNA abundance and patient sex, patient age, or tumour size (p > 0.05). However, there was significantly greater Ang-1 (p = 0.02), Ang-2 (p = 0.03), and Tie2 (p = 0.04) mRNA abundance in clear cell than in chromophil RCCs. Ang-2 gene expression was down-regulated by hypoxia in VHL wild-type RCC786-0 and RCC4 transfectants (p = 0.0002 and p = 0.04, respectively), mirroring the low expression in human tumour cells. These data suggest that it is endothelial induction of Ang-2 in tumours that regulates vessel stability and supports targeting Tie2 as an effective novel anti-angiogenic therapy in clear cell RCCs.
Intelligent Resource Management in Blockchain-Based Cloud Datacenters (2017)

Nowadays, more and more companies migrate business from their own servers to the cloud. With the influx of computational requests, datacenters consume tremendous energy every day, attracting great attention in the energy efficiency dilemma. In this paper, we investigate the energy-aware resource management problem in cloud datacenters, where green energy with unpredictable capacity is connected. Via proposing a robust blockchain-based decentralized resource management framework, we save the energy consumed by the request scheduler. Moreover, we propose a reinforcement learning method embedded in a smart contract to further minimize the energy cost. Because the reinforcement learning method is informed from the historical knowledge, it relies on no request arrival and energy supply. Experimental results on Google cluster traces and real-world electricity price show that our approach is able to reduce the datacenters cost significantly compared with other benchmark algorithms.
Novel gene rearrangements in transformed breast cells identified by high-resolution breakpoint analysis of chromosomal aberrations (2009)

Chromosomal copy number alterations and chromosomal rearrangements are frequent mutations in human cancer. Unlike copy number alterations, little is known about the role and occurrence of chromosomal rearrangements in breast cancer. This may be due to the fact that chromosome-based breakpoint analysis is widely restricted to cultured cells. In order to identify gene rearrangements in breast cancer, we studied the chromosomal breakpoints in radiation-transformed epithelial breast cell lines using a high-resolution array-based approach using 1 Mb bacterial artificial chromosome (BAC) arrays. The breakpoints were further narrowed down by fluorescence in situ hybridisation (FISH) with clones from the 32 k BAC library. The analysis of the cell lines B42-11 and B42-16 revealed rearrangements of chromosomes 7, 8, 10 and 12. We identified the genes Has2, Grid1, Ret, Cpm, Tbx3, Tbx5, Tuba1a, Wnt1 and Arf3 within the breakpoint regions. Quantitative RT-PCR showed a deregulated expression of all of these candidate genes except for Tbx5 and Tbx3. This is the first study demonstrating gene rearrangements and their deregulated mRNA expression in radiation-transformed breast cells. Since the gene rearrangements occurred in the transformed and tumourigenic cell lines only, it is likely that these were generated in conjunction with malignant transformation of the epithelial breast cells and therefore might reflect early molecular events in breast carcinogenesis. Initial studies indicate that these gene alterations are also found in sporadic breast cancers.
A data mining approach to reduce the false alarm rate of patient monitors (2012)

Patient monitors in intensive care units trigger alarms if the state of the patient deteriorates or if there is a technical problem, e.g. loose sensors. Monitoring systems have a high sensitivity in order to detect relevant changes in the patient state. However, multiple studies revealed a high rate of either false or clinically not relevant alarms. It was found that the high rate of false alarms has a negative impact on both patients and staff. In this study we apply data mining methods to reduce the false alarm rate of monitoring systems. We follow a multi-parameter approach where multiple signals of a monitoring system are used to classify given alarm situations. In particular we focus on five alarm types and let our system decide whether the triggered alarm is clinically relevant or can be considered as a false alarm. Several classification algorithms (Naive Bayes, Decision Trees, SVM, kNN and Multi-Layer Perceptron) were evaluated. For training and test sets a subset of the freely available MIMIC II database was used. Alarm-specific classification accuracy was between 78.56% and 98.84%. Suppression rates for false alarms were between 75.24% and 99.23%. Classification results strongly depend on available training data, which is still limited in the intensive care domain. However, this study shows that data mining methods are useful and applicable for alarm classification.
Searching Twitter: Separating the Tweet from the Chaff (2021)

Within the millions of digital communications posted in online social networks, there is undoubtedly some valuable and useful information. Although a large portion of social media content is considered to be babble, research shows that people share useful links, provide recommendations to friends, answer questions, and solve problems. In this paper, we report on a qualitative investigation into the different factors that make tweets ‘useful’ and ‘not useful’ for a set of common search tasks. The investigation found 16 features that help make a tweet useful, noting that useful tweets often showed 2 or 3 of these features. ‘Not useful’ tweets, however, typically had only one of 17 clear and striking features. Further, we saw that these features can be weighted as according to different types of search tasks. Our results contribute a novel framework for extracting useful information from real-time streams of social-media content that will be used in the design of a future retrieval system.
Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice (2009)

Derepression of transposable elements (TEs) in the course of epigenetic reprogramming of the mouse embryonic germline necessitates the existence of a robust defense that is comprised of PIWI/piRNA pathway and de novo DNA methylation machinery. To gain further insight into biogenesis and function of piRNAs, we studied the intracellular localization of piRNA pathway components and used the combination of genetic, molecular, and cell biological approaches to examine the performance of the piRNA pathway in germ cells of mice lacking Maelstrom (MAEL), an evolutionarily conserved protein implicated in transposon silencing in fruit flies and mice. Here we show that principal components of the fetal piRNA pathway, MILI and MIWI2 proteins, localize to two distinct types of germinal cytoplasmic granules and exhibit differential association with components of the mRNA degradation/translational repression machinery. The first type of granules, pi-bodies, contains the MILI-TDRD1 module of the piRNA pathway and is likely equivalent to the enigmatic "cementing material" first described in electron micrographs of rat gonocytes over 35 years ago. The second type of granules, piP-bodies, harbors the MIWI2-TDRD9-MAEL module of the piRNA pathway and signature components of P-bodies, GW182, DCP1a, DDX6/p54, and XRN1 proteins. piP-bodies are found predominantly in the proximity of pi-bodies and the two frequently share mouse VASA homolog (MVH) protein, an RNA helicase. In Mael-mutant gonocytes, MIWI2, TDRD9, and MVH are lost from piP-bodies, whereas no effects on pi-body composition are observed. Further analysis revealed that MAEL appears to specifically facilitate MIWI2-dependent aspects of the piRNA pathway including biogenesis of secondary piRNAs, de novo DNA methylation, and efficient downregulation of TEs. Cumulatively, our data reveal elaborate cytoplasmic compartmentalization of the fetal piRNA pathway that relies on MAEL function.
Biodegradable stents: they do their job and disappear. (2006)

Despite the development and progression of metallic stents, many concerns still remain because of their permanent nature. Although metallic stents are effective in preventing recoil and late restenosis after coronary angioplasty, they continue to have limitations such as stent thrombosis and mismatch of the stent to the vessel size. Thus, the concept of bioabsorbable stents has emerged as an alternative to permanent metal stents. This review will outline concepts, material designs, preclinical, and initial clinical experimental studies with bioabsorbable stents.
A synthetic mammalian gene circuit reveals antituberculosis compounds (2008)

Synthetic biology provides insight into natural gene-network dynamics and enables assembly of engineered transcription circuitries for production of difficult-to-access therapeutic molecules. In Mycobacterium tuberculosis EthR binds to a specific operator (O(ethR)) thereby repressing ethA and preventing EthA-catalyzed conversion of the prodrug ethionamide, which increases the resistance of the pathogen to this last-line-of-defense treatment. We have designed a synthetic mammalian gene circuit that senses the EthR-O(ethR) interaction in human cells and produces a quantitative reporter gene expression readout. Challenging of the synthetic network with compounds of a rationally designed chemical library revealed 2-phenylethyl-butyrate as a nontoxic substance that abolished EthR's repressor function inside human cells, in mice, and within M. tuberculosis where it triggered derepression of ethA and increased the sensitivity of this pathogen to ethionamide. The discovery of antituberculosis compounds by using synthetic mammalian gene circuits may establish a new line of defense against multidrug-resistant M. tuberculosis.
The Art of Computer Programming, Volume 4, Fascicle 6: Satisfiability (2015)

This multivolume work on the analysis of algorithms has long been recognized as the definitive description of classical computer science. The four volumes published to date already comprise a unique and invaluable resource in programming theory and practice. Countless readers have spoken about the profound personal influence of Knuths writings. Scientists have marveled at the beauty and elegance of his analysis, while practicing programmers have successfully applied his cookbook solutions to their day-to-day problems. All have admired Knuth for the breadth, clarity, accuracy, and good humor found in his books. To continue the fourth and later volumes of the set, and to update parts of the existing volumes, Knuth has created a series of small books called fascicles, which are published at regular intervals. Each fascicle encompasses a section or more of wholly new or revised material. Ultimately, the content of these fascicles will be rolled up into the comprehensive, final versions of each volume, and the enormous undertaking that began in 1962 will be complete. Volume 4 Fascicle 6 This fascicle, brimming with lively examples, forms the middle third of what will eventually become hardcover Volume 4B. It introduces and surveys Satisfiability, one of the most fundamental problems in all of computer science: Given a Boolean function, can its variables be set to at least one pattern of 0s and 1s that will make the function true? Satisfiability is far from an abstract exercise in understanding formal systems. Revolutionary methods for solving such problems emerged at the beginning of the twenty-first century, and theyve led to game-changing applications in industry. These so-called SAT solvers can now routinely find solutions to practical problems that involve millions of variables and were thought until very recently to be hopelessly difficult. Fascicle 6 presents full details of seven different SAT solvers, ranging from simple algorithms suitable for small problems to state-of-the-art algorithms of industrial strength. Many other significant topics also arise in the course of the discussion, such as bounded model checking, the theory of traces, Las Vegas algorithms, phase changes in random processes, the efficient encoding of problems into conjunctive normal form, and the exploitation of global and local symmetries. More than 500 exercises are provided, arranged carefully for self-instruction, together with detailed answers.
DoveNet: Deep Image Harmonization via Domain Verification (2020)

Image composition is an important operation in image processing, but the inconsistency between foreground and background significantly degrades the quality of composite image. Image harmonization, aiming to make the foreground compatible with the background, is a promising yet challenging task. However, the lack of high-quality publicly available dataset for image harmonization greatly hinders the development of image harmonization techniques. In this work, we contribute an image harmonization dataset iHarmony4 by generating synthesized composite images based on COCO (resp., Adobe5k, Flickr, day2night) dataset, leading to our HCOCO (resp., HAdobe5k, HFlickr, Hday2night) sub-dataset. Moreover, we propose a new deep image harmonization method DoveNet using a novel domain verification discriminator, with the insight that the foreground needs to be translated to the same domain as background. Extensive experiments on our constructed dataset demonstrate the effectiveness of our proposed method. Our dataset and code are available at https://github.com/bcmi/Image_Harmonization_Datasets.
An investigation on speaker vector-based speaker identification under noisy conditions (2008)

This paper presents the speaker identification method based on a speaker vector under noisy conditions. The aim of this work is to improve the performance of the speaker identification under noisy conditions. The identification system is based on the method of anchor models. In this system, the location of each speaker is represented by the speaker vector which consists of the set of the likelihood between a target utterance and the anchor models. Since the acoustic model of the target is not needed, speaker identification can be performed with a very short reference speech (5.5sec average). In order to achieve the improvement, the structure of anchor models was investigated. Evaluations were performed on 8 or 30-speaker identification task in Japanese. The results showed that a speaker identification rate of 70.98\% has been obtained by using phonetic-class structured GMMs (pcs_GMMs) as anchor models under noisy conditions.
Durability of All-Solid-State Switchable Mirror Based on Magnesium–Nickel Thin Film (2007)

An all-solid-state switchable mirror with thin film was prepared for basic research on a new type of smart window. The device has a multilayer of /indium tin oxide/glass and can switch reversibly from a reflective state to a transparent one. The durability of the device was investigated by a cyclic switching test. Though a transmittance change was slightly decreased, the device showed high durability up to 2000 switching cycles. We found that the degradation was related with the damaged surface of thin film and the diffusion of Ni and Pd atoms into thin film during a cyclic switching test.
A Rapid, Quantitative Fluorescence Assay for Cell Damage by Cytotoxic Antibodies (1970)

Abstract Our laboratory recently (1) described a fluorochromatic assay for cell damage by cytotoxic alloantibody, which was based on retention of fluorescein by intact cells after its hydrolysis from fluorescein diacetate esters (FDA) (2). Although the method gave reproducible results in our hands, it was slow and always subject to error, since traces of complement used in the reaction were capable of hydrolyzing FDA, thus yielding erroneously high values of cell viability. This was not satisfactory and accordingly we sought another approach to differential fluorescent staining of cells, which would still allow machine-reading of the assays. Rather than looking for other compounds that were enzymatically changed from non-fluorescent to fluorescent, we chose to screen a number of fluorescent probes (3), compounds whose fluorescence is enhanced when bound to protein or nucleic acids. Such compounds were initially screened by observing fresh and heat-damaged lymphocytes, bathed in solutions of various probes, with the fluorescence microscope.On the basis of this screening we selected ethidium bromide, a compound which had previously been used to quantitate DNA in solution (4). The dye, when dissolved in phosphatebuffered isotonic saline in concentrations of about 1 µg/ml, penetrates intact cells slowly but rapidly enters damaged eells. Upon entry it forms a bright red fluorescent complex with the nucleus. The intensity of this fluorescence may be read on a fluorometer and is proportional to the degree of damage within the cell population examined. Although greatest sensitivity has been obtained using a specially-modified red-sensitive fluorometer, the method may be applied to other instruments. The speed, simpIicity and reproducibility of the method appear to make it worthwhile for determining cytotoxic antibody,
Cancer-specific binding of a mouse MAb vs. Candida krusei cytochrome c: an antigen recognized by a cancer-associated human MAb HB4C5 (1993)

More than 60 mouse monoclonal antibodies directed to cytochrome c from Candida krusei with different specificities were raised. Most of these monoclonal antibodies, except for three of them, did not cross-react with bovine cytochrome c. By the immunoblotting method, the monoclonal antibodies of clones HCC 5-13, 9-2, and 10-5 reacted with the Candida cytochrome c, which had been transferred onto nitrocellulose membrane, but those of clones HCC 1-22, 6-3, and 17-3 did not, although all these monoclonal antibodies strongly reacted with coated Candida cytochrome c on plastic immunoplates when examined by ELISA. On the contrary, monoclonal antibody activities of clones HCC 1-22, 6-3, and 17-3 in binding to the coated cytochrome c in ELISA were inhibited competitively by the addition of extra Candida cytochrome c, whereas those of clones HCC 5-13, 9-2, and 10-5 were not inhibited. Among these monoclonal antibodies, the antibody of clone HCC 6-3, which showed a good reactivity to added cytochrome c in inhibiting ELISA reaction but was not reactive with the transblotted cytochrome c on nitrocellulose, was found to be reactive with human lung cancer tissues specifically with no reactivity to normal tissues. The immunostaining of lung cancer tissue showed that this mouse monoclonal antibody to Candida cytochrome c reacted to the cytoplasmic fraction of the cancer cells specifically.
Simulated autohydrolysis of aspen milled wood lignin in the presence of aromatic additives. Changes in molecular weight distribution (1980)

The reactions between aspen milled wood lignin (MWL) and 2-naphthol, resorcinol, and p-hydroxybenzoic acid were studied under simulated autohydrolysis conditions. The material after the reaction was separated into a dioxane-insoluble fraction (DI), a dioxane-soluble but ether-insoluble fraction (DSEI), and an ether-soluble fraction (ES). In the absence of additive, the lignin first depolymerized and remained solvent soluble, then repolymerized to become insoluble. With 2-naphthol as additive, the amount of DI lignin decreased proportionally to the amount of additive present. When more than 0.1 mole of 2-naphthol/C-9 unit was present, no DI lignin was formed, that is, all the lignin was soluble. Gel permeation chromatography studies indicated that the additive was acting effectively as a blocking agent, preventing lignin repolymerization. Small amounts of resorcinol acted as a repolymerizing agent since two or more fragments of lignin could readily condense with a molecule of the very active additive. As a result of this bridging effect, the amount of DI lignin increased. As the amount of resorcinol was increased, it behaved more like a blocking agent and a reduction in the amount of DI lignin was observed. The presence of a large excess of resorcinol resulted in the formation of soluble lignin only. The molecular weight distributions supported the proposed dual role of resorcinol as a bridging or blocking agent. The use of an excess of p-hydroxybenzoic acid prevented the formation of DI material and resulted in low molecular weight soluble lignin.
Ultra-thin silicon dioxide leakage current and scaling limit (2003)

Modifications are made to Fowler-Nordheim tunneling current analysis to model accurately the measured conduction characteristics of insulator layers thinner than 6 nm. The most significant is direct tunneling for which a closed-form expression is introduced. Polysilicon depletion and electron wave interference are also considered. 4 nm is found to a practical limit for SiO/sub 2/ scaling in VLSI applications due to direct tunneling leakage almost independent of power supply voltage. The convergence of the intrinsic TDDB and gate leakage criteria is established and the possibility that gate leakage will set the ultimate limit to oxide scaling at 4 nm is suggested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
[Diagnostic value of total plasma levels of bile acids and ammonia in liver diseases in sheep]. (1998)

For the estimation of the diagnostic value of plasma concentrations of total bile acids and ammonia in liver disease healthy controls (n = 23) as well as animals sick with different diseases were examined. The reference values for total bile acids and ammonia in the plasma of sheep range from 18-166 mumol/l and 15-64 mumol/l, respectively. While animals with chronic copper poisoning (n = 18), vitamin E/selenium deficiency (n = 15) and with diseases not affecting the liver (n = 8) did not show significant differences in concentrations of total bile acids and ammonia from those of the healthy controls, this could be proven for animals with severe hepatopathy or hepatoencephalopathy. Furthermore, some of the latter group showed increased ammonia concentrations in the liquor cerebrospinalis and multifocal vacuolation of the central nervous system. The determination of total bile acids and ammonia in the diagnosis of liver disease in sheep would also be useful. The hepatoencephalic syndrome should therefore be considered as possible differential diagnosis in animals showing neurological signs.
ChemInform Abstract: CYCLOADDUCTS OF PHENYLSULFONYL CYANIDE N‐OXIDE AND N‐SUBSTITUTED 1,2‐DIHYDROPYRIDINES. REGIO‐ AND STEREOSPECIFICITY (1984)

Abstract Aus den Dihydropyridinen (I) erhält Inun mit dem in situ Ilcrgeslelltcn PhenylsulfonyInitriloxid (H) regiospezifisch die Adduk‐ Ie (III).