gebhart/patrepeval huggingface dataset:
DNA looping induced by a transcriptional enhancer in vivo (2005)

Enhancers are DNA sequences that can activate gene transcription from remote positions. In yeast, regulatory sequences that are functionally equivalent to the metazoan enhancers are called upstream activating sequences (UASs). UASs show a lower degree of flexibility than their metazoan counterparts, but can nevertheless activate transcription from a distance of >1000 bp from the promoter. One of several models for the mechanism of action of transcriptional enhancers proposes that enhancer-bound activating proteins contact promoter-bound transcription factors and thereby get in close proximity to the promoter region with concomitant looping of the intervening DNA. We tested the mode of enhancer activity in yeast. A polymerase II-transcribed gene was paired with a remote, inducible enhancer. An independent reporter system was inserted next to the promoter to monitor the potential modes of enhancer activity. Our results show that the enhancer activated the reporter system only in the presence of a functional promoter. We also demonstrate that the heterologous expression of GAGA, a factor known to facilitate DNA loop formation, allows enhancer action in yeast over a distance of 3000 bp.
Identification of a New Member of the Tryptase Family of Mouse and Human Mast Cell Proteases Which Possesses a Novel COOH-terminal Hydrophobic Extension (1999)

Mapping of the tryptase locus on chromosome 17 revealed a novel gene 2.3 kilobase 3' of the mouse mast cell protease (mMCP) 6 gene. This 3.7-kilobase gene encodes the first example of a protease in the tryptase family that contains a membrane-spanning segment located at its COOH terminus. Comparative structural studies indicated that the putative transmembrane tryptase (TMT) possesses a unique substrate-binding cleft. As assessed by RNA blot analyses, mTMT is expressed in mice in both strain- and tissue-dependent manners. Thus, different transcriptional and/or post-transcriptional mechanisms are used to control the expression of mTMT in vivo. Analysis of the corresponding tryptase locus in the human genome resulted in the isolation and characterization of the hTMT gene. The hTMT transcript is expressed in numerous tissues and is also translated. Analysis of the tryptase family of genes in mice and humans now indicates that a primordial serine protease gene duplicated early and often during the evolution of mammals to generate a panel of homologous tryptases in each species that differ in their tissue expression, substrate specificities, and physical properties.
An Automated Multiple-Choice Question Generation using Natural Language Processing Techniques (2021)

Automatic multiple-choice question generation (MCQG) is a useful yet challenging task in Natural Language Processing (NLP). It is the task of automatic generation of correct and relevant questions from textual data. Despite its usefulness, manually creating sizeable, meaningful and relevant questions is a time-consuming and challenging task for teachers. In this paper, we present an NLP-based system for automatic MCQG for Computer-Based Testing Examination (CBTE).We used NLP technique to extract keywords that are important words in a given lesson material. To validate that the system is not perverse, five lesson materials were used to check the effectiveness and efficiency of the system. The manually extracted keywords by the teacher were compared to the auto-generated keywords and the result shows that the system was capable of extracting keywords from lesson materials in setting examinable questions. This outcome is presented in a user-friendly interface for easy accessibility.
Glycemic Treatment in Type 1 and Type 2 Diabetes (2006)

This is the second in a series of articles on presentations at the American Diabetes Association’s 66th Scientific Sessions, Washington, DC, 9–13 June 2006.

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At the meeting of the Council on Nutritional Science and Metabolism, Joan V.C. Hill (Natick, MA) introduced a session addressing the implications of postprandial blood glucose monitoring by reminding the audience that the American Diabetes Association (ADA) recommends a target HbA1c (A1C) of ≤7% but that the most recent National Health and Nutrition Examination Survey suggests that >60% of persons with diabetes fail to meet this goal. In a Quest laboratories analysis of 14.3 million A1C tests performed for diabetes diagnosis codes, half were shown to be above goal, although the average decreased from 7.8% in 2001 to 7.2% in 2005. An important question is the contribution of postprandial blood glucose to A1C, with the corollary being the determination of reasonable postprandial blood glucose targets, with Hill asking whether targeting postprandial blood glucose can improve metabolic control or, more importantly, improve outcome, recognizing the difficulty of determining the relationship between postprandial blood glucose and outcome. “The clear message,” Hill concluded, is that “achieving A1C close to goal [will require] monitoring postprandial glucose.”

Martin Abrahamson (Boston, MA) reminded the audience, “Most of our lives are spent in the postprandial state,” with the preprandial state not beginning until 10 h after ingestion of food, perhaps in most persons only from 4:00 to 8:00 a.m. Thus, measurement of fasting glucose may represent a state not particularly representative of that encountered through the day. To achieve the target goal of A1C as close to normal …
Very Large Scale Integration of Nanopatterned YBa<sub>2</sub>Cu<sub>3</sub>O<sub>7−δ</sub> Josephson Junctions in a Two-Dimensional Array (2009)

Very large scale integration of Josephson junctions in a two-dimensional series-parallel array has been achieved by ion irradiating a YBa(2)Cu(3)O(7-delta) film through slits in a nanofabricated mask created with electron beam lithography and reactive ion etching. The mask consisted of 15820 high aspect ratio (20:1), 35 nm wide slits that restricted the irradiation in the film below to form Josephson junctions. Characterizing each parallel segment k, containing 28 junctions, with a single critical current I(ck) we found a standard deviation in I(ck) of about 16%.
SPL7013 Gel as a Topical Microbicide for Prevention of Vaginal Transmission of SHIV <sub>89.6P</sub> in Macaques (2005)

SPL7013 is a dendrimer with a polyanionic outer surface that allows multiple interactions with target sites. It potently binds and blocks HIV-1 and chimeric simian/HIV-1 viruses (SHIVs) replication in vitro. Gels containing different concentrations of SPL7013 were used as topical microbicides in female pigtailed macaques (Macaca nemestrina) to study their ability to prevent vaginal transmission of SHIV(89,6P). On virus challenge, all untreated macaques (8/8) and seven of eight macaques treated with placebo gel were infected within 2 weeks postinfection (PI) and showed high plasma viremia and dramatic CD4(+) cell decline within 4 weeks PI. In contrast, 6/6 macaques, 5/6 macaques, and 2/6 macaques treated with 5% w/w (50 mg/ml), 3% w/w (30 mg/ml), and 1% w/w (10 mg/ml) SPL7013 gels, respectively, resisted viral challenge. The results showed that animals treated with SPL7013 showed a dose-dependent resistance to virus challenge. Neither SPL7013 nor placebo gels produced any adverse effects following the single application in the study. These results showed that 3-5% w/w SPL7013 gels were effective in blocking vaginal transmission of SHIV in macaques after single gel application followed by single virus challenge. These results suggest that SPL7013 gel may be a promising anti-HIV microbicide formulation for further evaluation.
Field trial of a quantum secured 10 Gb/s DWDM transmission system over a single installed fiber (2014)

We present results from the first field-trial of a quantum-secured DWDM transmission system, in which quantum key distribution (QKD) is combined with 4 × 10 Gb/s encrypted data and transmitted simultaneously over 26 km of field installed fiber. QKD is used to frequently refresh the key for AES-256 encryption of the 10 Gb/s data traffic. Scalability to over 40 DWDM channels is analyzed.
Mathematical framework for large-scale brain network modeling in The Virtual Brain (2015)

In this article, we describe the mathematical framework of the computational model at the core of the tool The Virtual Brain (TVB), designed to simulate collective whole brain dynamics by virtualizing brain structure and function, allowing simultaneous outputs of a number of experimental modalities such as electro- and magnetoencephalography (EEG, MEG) and functional Magnetic Resonance Imaging (fMRI). The implementation allows for a systematic exploration and manipulation of every underlying component of a large-scale brain network model (BNM), such as the neural mass model governing the local dynamics or the structural connectivity constraining the space time structure of the network couplings. Here, a consistent notation for the generalized BNM is given, so that in this form the equations represent a direct link between the mathematical description of BNMs and the components of the numerical implementation in TVB. Finally, we made a summary of the forward models implemented for mapping simulated neural activity (EEG, MEG, sterotactic electroencephalogram (sEEG), fMRI), identifying their advantages and limitations.
Model-Based Air-Fuel Ratio Control in SI Engines with a Switch-Type EGO Sensor (1994)

<div class="htmlview paragraph">High bandwidth control of the air-fuel ratio is necessary in order to minimize the exhaust emissions of spark-ignition engines with three-way catalytic converters. A new approach is to implement a control structure based on modern control and estimation theory. This work describes the implementation of an estimator-based controller which uses the feedback from an on-off zirconia exhaust oxygen sensor of the type currently used in production vehicles. The limit-cycle associated with the on-off oxygen sensor in conventional systems is eliminated with the estimator-based control structure. Furthermore, the in-cylinder air-fuel ratio tracks the commanded value, so that if a limit cycle is desired in some areas of the engine's operating range for better catalyst operation, its amplitude and frequency can be set arbitrarily.</div>
Control by state observer of PEMFC anodic purges in dead-end operating mode (2015)

International audience
Mapping the Thermal Behavior of DNA Origami Nanostructures (2013)

Understanding the thermodynamic properties of complex DNA nanostructures, including rationally designed two- and three-dimensional (2D and 3D, respectively) DNA origami, facilitates more accurate spatiotemporal control and effective functionalization of the structures by other elements. In this work fluorescein and tetramethylrhodamine (TAMRA), a Förster resonance energy transfer (FRET) dye pair, were incorporated into selected staples within various 2D and 3D DNA origami structures. We monitored the temperature-dependent changes in FRET efficiency that occurred as the dye-labeled structures were annealed and melted and subsequently extracted information about the associative and dissociative behavior of the origami. In particular, we examined the effects of local and long-range structural defects (omitted staple strands) on the thermal stability of common DNA origami structures. The results revealed a significant decrease in thermal stability of the structures in the vicinity of the defects, in contrast to the negligible long-range effects that were observed. Furthermore, we probed the global assembly and disassembly processes by comparing the thermal behavior of the FRET pair at several different positions. We demonstrated that the staple strands located in different areas of the structure all exhibit highly cooperative hybridization but have distinguishable melting temperatures depending on their positions. This work underscores the importance of understanding fundamental aspects of the self-assembly of DNA nanostructures and can be used to guide the design of more complicated DNA nanostructures, to optimize annealing protocol and manipulate functionalized DNA nanostructures.
A stochastic case frame approach for natural language understanding (2002)

A stochastically based approach for the semantic analysis component of a natural spoken language system for the ARPA Air Travel Information Services (ATIS) task has been developed. The semantic analyzer of the spoken language system already in use at LIMSI makes use of a rule-based case grammar. In this work, the system of rules for the semantic analysis is replaced with a relatively simple first-order hidden Markov model. The performances of the two approaches can be compared because they use identical semantic representations, despite their rather different methods for meaning extraction. We use an evaluation methodology that assesses performance at different semantic levels, including the database response comparison used in the ARPA ATIS paradigm.
Breast cancer prediction and the Wolfe classification of mammograms (1985)

Mammographic parenchymal patterns have been proposed as a method of determining women at high risk of developing breast cancer. Wolfe's original report of relative risks as high as 37:1 for "dysplastic" breasts (DY) as compared with adipose breasts (N1), with intermediate values of P1 and P2, were not uniformly confirmed by others. (Relative risks are used here as the equivalent of odds ratios.) A case-control study of 706 breast cancers, each with two matching controls, drawn from 40,000 participants in four Breast Cancer Detection Demonstration Project clinics, was conducted to assess the role of the Wolfe classification of breast parenchymal patterns as a breast-cancer risk factor together with a set of well-established risk factors for breast cancer. Relative risks of 3.1 for DY to N1, 3.5 for P2 to N1, and 2.0 for P1 to N1 were determined. These are comparable to or greater than other known risk factors found in the same population. The Wolfe classification of parenchymal patterns strengthens the basis for clinical judgment, but should not be used exclusively to determine intervention in an individual patient's care. (<i>JAMA</i>1985;254:1050-1053)
Inhibition of proliferation of small intestinal and bronchopulmonary neuroendocrine cell lines by using peptide analogs targeting receptors (2008)

The data demonstrate GH-RH antagonists or peptide-linked antineoplastic agents such as AN-152 and AN-238 are effective inhibitors of NET proliferation in vitro. Because peptide receptors such as those for GH-RH, LH-RH, and SST subtypes are commonly expressed by NETs, the development of antineoplastic agents targeted to specific tumor receptors may provide a more efficacious strategy than systemic chemotherapeutic agents currently in use.
Regulation of the xanthophyll cycle pool size in duckweed (<i>Lemna minor</i>) plants (2002)

Duckweed (Lemna minor L.) plants grown under high light are characterized, when compared to low light acclimated plants, by a higher xanthophyll cycle (VAZ) pool content, but also by a higher proportion of photoconvertible violaxanthin and a superior ability to synthesize VAZ pigments. When duckweed plants were transferred to a high light environment a general response was the quick adjustment of the carotenoid composition, mainly xanthophyll cycle pigments. These changes resulted from a balance between a process of continuous light-independent carotenoid degradation and a light-induced accumulation. The use of norflurazon, an inhibitor of carotenogenesis, allowed us to demonstrate that the observed light induced increase of the VAZ pool was mainly caused by de novo synthesis through carotenogenesis. The extent of light-induced carotenogenesis was proportional to the light treatment and also to the operation of the VAZ cycle since it was partly abolished by treatments leading to a low activity of the VAZ cycle, such as low light, DTT or DCMU. These results suggest that not only the light itself, but also a mechanism triggered by a factor associated with the de-epoxidation state of the VAZ cycle controls carotenogenesis at some point before phytoene formation in the terpenoid biosynthesis pathway.
Mitochondrial dysfunction in amyotrophic lateral sclerosis – a valid pharmacological target? (2013)

Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease characterized by the selective death of upper and lower motor neurons which ultimately leads to paralysis and ultimately death. Pathological changes in ALS are closely associated with pronounced and progressive changes in mitochondrial morphology, bioenergetics and calcium homeostasis. Converging evidence suggests that impaired mitochondrial function could be pivotal in the rapid neurodegeneration of this condition. In this review, we provide an update of recent advances in understanding mitochondrial biology in the pathogenesis of ALS and highlight the therapeutic value of pharmacologically targeting mitochondrial biology to slow disease progression.
A Study of Measurement Interference in the Optoacoustic Detection of NO<sub>2</sub> by Argon-Ion Laser Excitation (1982)

Optoacoustic measurements of NO 2 excited by an Ar + laser were performed in the presence of NO, N 2 , H 2 O, and O 2 matrix gases. Identical sensitivities were measured in all matrix gases except O 2 where energy transfer from NO 2 to the metastable O 2 ( 1 Δ g ) state resulted in a dramatic decrease in sensitivity.
Trastuzumab-induced cardiotoxicity in early breast cancer: Evaluation of possible risk and protective factors. (2012)

e11054 Background: Adjuvant trastuzumab improves survival in early breast cancer (EBC) patients (pts). However, trastuzumab-induced cardiotoxicity (TIC) renders it necessary to identify possible risk and protective factors. Methods: A retrospective study was conducted in which medical charts of pts treated with adjuvant trastuzumab were reviewed. Hypertension, smoking history, dysthyroidism, obesity, hypercholesterolemia, diabetes mellitus and anthracycline cumulative dose were considered as potential risk factors. The relationship between the use of beta-blockers (BB), angiotensin-converting enzyme inhibitors (ACEI) and/or angiotensin receptor blockers (ARB) (either started before or during adjuvant therapy) and TIC development was also evaluated. TIC was defined as an absolute left ventricular ejection fraction (LVEF) decrease ≥15 points from baseline or an absolute LVEF <50%. The term heart failure (HF) referred to the New York Heart Association classification III or IV. Logistic regression was used to assess relative risks. Results: A total of 179 HER2-positive EBC pts (median 54 years, range 30-84) were evaluated. 154 (86%) were treated with anthracycline-based adjuvant chemotherapy. 78 (44%) did not show any risk factors, whereas 101 (56%) had at least one: hypertension (24%), smoking habit (16%), dysthyroidism (18%), obesity (12%), hypercholesterolemia (9%) and diabetes mellitus (4%). Among the 179 EBC pts, 78 (44%, 95% confidence intervals (CI) 37-51%) experienced TIC during their 12-month trastuzumab treatment and only 4 (2%, 95% CI 0-4%) developed HF. 14 pts stopped trastuzumab due to TIC. None of the risk factors described above was correlated with TIC development. A previous anthracycline cumulative dose > 240 mg/m 2 conferred an odds ratio of 3.07 compared with treatmemt with lower doses (95% CI 1.29-7.27, p=0.0011). BB, ACEI and/or ARB neither reduced nor increased the risk of TIC. Conclusions: TIC is a frequent, albeit generally mild, adverse event in clinical practice. Closer collaboration between cardiologists and oncologists is needed to better define risk and protective factors of cardiotoxicity in order to avoid trastuzumab-therapy discontinuation.
Spontaneous human lymphocyte‐mediated cytotoxicity againts tumour target cells. I. The effect of malignant disease (1976)

Spontaneous human lymphocyte-mediated cytotoxicity (SLMC) against tumour-cell targets was examined in a series of patients with localized or malignant disease, both treated and untreated, and patients with untreated chronic lymphocytic leukemia (CLL). The level of SLMC was assessed by means of two previously established assay systems; the xenogeneic assay involving the mouse mastocytoma line P815, and the allogeneic assay in which the human chronic myelogenous leukemia-derived line, K562, was used. The assay systems involve the use of Ficoll-Isopaque-separated, iron-plus-magnetism-purified lymphocytes in an overnight 51chromium release assay, and reflect the cytotoxic ability of human non-T, complement receptor-, Fc receptor-positive lymphocytes. In the present paper, lymphocytes from all normal donors tested showed significant activity in the SLMC assay, with some variation from day to day. This variation was markedly reduced when different normal donors were tested on the same day and under identical experimental conditions. In contrast, lymphocytes from many patients with malignant disease had decreased SLM activity, and this decrease was highly significant in patients with treated or untreated metastatic disease, or untreated CLL. This was also the case when the data were expressed relative to the number of cytotoxic cells in the normal control population, or in comparison to the relative SLMC activity of lymphocytes from patients with other conditions. Markedly decreased SLMC was observed in some patients in spite of normal T and B lymphocyte proportions, or the presence of the ability to mount a vigorous delayed hypersensitivity reaction to PPD. A comparison of the xenogeneic and allogeneic assays showed that the same information with respect to whether SLMC was normal or abnormal was obtained with both assays in the majority of cases. The significance of the data is discussed with respect to the possible role of SLMC in vivo and the relevance of SLMC to the assessment of specific cell-mediated cytotoxicity in malignant disease.
CSRNet: Dilated Convolutional Neural Networks for Understanding the Highly Congested Scenes (2018)

We propose a network for Congested Scene Recognition called CSRNet to provide a data-driven and deep learning method that can understand highly congested scenes and perform accurate count estimation as well as present high-quality density maps. The proposed CSRNet is composed of two major components: a convolutional neural network (CNN) as the front-end for 2D feature extraction and a dilated CNN for the back-end, which uses dilated kernels to deliver larger reception fields and to replace pooling operations. CSRNet is an easy-trained model because of its pure convolutional structure. We demonstrate CSRNet on four datasets (ShanghaiTech dataset, the UCF_CC_50 dataset, the WorldEXPO'10 dataset, and the UCSD dataset) and we deliver the state-of-the-art performance. In the ShanghaiTech Part_B dataset, CSRNet achieves 47.3% lower Mean Absolute Error (MAE) than the previous state-of-the-art method. We extend the targeted applications for counting other objects, such as the vehicle in TRANCOS dataset. Results show that CSRNet significantly improves the output quality with 15.4% lower MAE than the previous state-of-the-art approach.