gebhart/patrepeval huggingface dataset:
rib-2, a Caenorhabditis elegans Homolog of the Human Tumor Suppressor EXT Genes Encodes a Novel α1,4-N-Acetylglucosaminyltransferase Involved in the Biosynthetic Initiation and Elongation of Heparan Sulfate (2001)

The proteins encoded by the EXT1, EXT2, and EXTL2 genes, members of the hereditary multiple exostoses gene family of tumor suppressors, are glycosyltransferases required for the heparan sulfate biosynthesis. Only two homologous genes, rib-1 and rib-2, of the mammalian EXT genes were identified in the Caenorhabditis elegans genome. Although heparan sulfate is found in C. elegans, the involvement of the rib-1 and rib-2 proteins in heparan sulfate biosynthesis remains unclear. In the present study, the substrate specificity of a soluble recombinant form of the rib-2 protein was determined and compared with those of the recombinant forms of the mammalian EXT1, EXT2, and EXTL2 proteins. The present findings revealed that the rib-2 protein was a unique alpha1,4-N-acetylglucosaminyltransferase involved in the biosynthetic initiation and elongation of heparan sulfate. In contrast, the findings confirmed the previous observations that both the EXT1 and EXT2 proteins were heparan sulfate copolymerases with both alpha1,4-N-acetylglucosaminyltransferase and beta1,4-glucuronyltransferase activities, which are involved only in the elongation step of the heparan sulfate chain, and that the EXTL2 protein was an alpha1,4-N-acetylglucosaminyltransferase involved only in the initiation of heparan sulfate synthesis. These findings suggest that the biosynthetic mechanism of heparan sulfate in C. elegans is distinct from that reported for the mammalian system.
Nonconventional Odd-Denominator Fractional Quantum Hall States in the Second Landau Level (2010)

We report the observation of a new fractional quantum Hall state in the second Landau level of a two-dimensional electron gas at the Landau level filling factor ν=2+6/13. We find that the model of noninteracting composite fermions can explain the magnitude of gaps of the prominent 2+1/3 and 2+2/3 states. The same model fails, however, to account for the gaps of the 2+2/5 and the newly observed 2+6/13 states suggesting that these two states are of exotic origin.
Learning Important Features Through Propagating Activation Differences (2017)

The purported "black box" nature of neural networks is a barrier to adoption in applications where interpretability is essential. Here we present DeepLIFT (Deep Learning Important FeaTures), a method for decomposing the output prediction of a neural network on a specific input by backpropagating the contributions of all neurons in the network to every feature of the input. DeepLIFT compares the activation of each neuron to its 'reference activation' and assigns contribution scores according to the difference. By optionally giving separate consideration to positive and negative contributions, DeepLIFT can also reveal dependencies which are missed by other approaches. Scores can be computed efficiently in a single backward pass. We apply DeepLIFT to models trained on MNIST and simulated genomic data, and show significant advantages over gradient-based methods. Video tutorial: http://goo.gl/qKb7pL, ICML slides: bit.ly/deeplifticmlslides, ICML talk: https://vimeo.com/238275076, code: http://goo.gl/RM8jvH.
The EPS Matrix: The “House of Biofilm Cells” (2007)

In response to a suggestion by the Biofilms 2007 organizing committee to hold an evening session on biofilm extracellular polymeric substances (EPS), an exceptionally inspiring event followed contributions by Ken Bayles, Alan Decho, Martina Hausner, Jan Kreft, Thomas Neu, Per Nielsen, Ute Romling,
Polarization sensitive optical coherence tomography – a review [Invited] (2017)

Optical coherence tomography (OCT) is now a well-established modality for high-resolution cross-sectional and three-dimensional imaging of transparent and translucent samples and tissues. Conventional, intensity based OCT, however, does not provide a tissue-specific contrast, causing an ambiguity with image interpretation in several cases. Polarization sensitive (PS) OCT draws advantage from the fact that several materials and tissues can change the light's polarization state, adding an additional contrast channel and providing quantitative information. In this paper, we review basic and advanced methods of PS-OCT and demonstrate its use in selected biomedical applications.
Acute thrombocytopenia after treatment with tirofiban or eptifibatide is associated with antibodies specific for ligand-occupied GPIIb/IIIa (2002)

Acute thrombocytopenia is a recognized complication of treatment with GPIIb/IIIa inhibitors whose cause is not yet known. We studied 9 patients who developed severe thrombocytopenia (platelets less than 25 x 10(9)/L) within several hours of treatment with the GPIIb/IIIa inhibitors tirofiban (4 patients) and eptifibatide (5 patients). In each patient, acute-phase serum contained a high titer (range, 1:80-1:20 000) IgG antibody that reacted with the glycoprotein IIb/IIIa complex only in the presence of the drug used in treatment. Four patients had been previously treated with the same drug, but 5 had no known prior exposure. Pretreatment serum samples from 2 of the latter patients contained drug-dependent antibodies similar to those identified after treatment. No tirofiban- or eptifibatide-dependent antibodies were found in any of 100 randomly selected healthy blood donors, and only 2 of 23 patients receiving tirofiban or eptifibatide who did not experience significant thrombocytopenia had extremely weak (titer, 1:2) tirofiban-dependent antibodies. In preliminary studies, evidence was obtained that the 9 antibodies recognize multiple target epitopes on GPIIb/IIIa complexed with the inhibitor to which the patient was sensitive, indicating that they cannot all be specific for the drug-binding site. The findings indicate that acute thrombocytopenia after the administration of tirofiban or eptifibatide can be caused by drug-dependent antibodies that are "naturally occurring" or are induced by prior exposure to drug. These antibodies may be human analogs of mouse monoclonal antibodies that recognize ligand-induced binding sites (LIBS) induced in the GPIIb/IIIa heterodimer when it reacts with a ligand-mimetic drug.
Homo‐oligomer formation by basigin, an immunoglobulin superfamily member, via its N‐terminal immunoglobulin domain (2000)

Basigin (Bsg) is a highly glycosylated transmembrane protein with two immunoglobulin (Ig)-like domains. A number of studies, including gene targeting, have demonstrated that Bsg plays pivotal roles in spermatogenesis, implantation, neural network formation and tumor progression. In the present study, to understand the mechanism of action of Bsg, we determined its expression status on the plasma membrane. Cotransfection of Bsg expression vectors with two different tags clarified that Bsg forms homo-oligomers in a cis-dependent manner on the plasma membrane. If the disulfide bond of the more N-terminally located Ig-like domain was destroyed by mutations, Bsg could not form oligomers. In contrast, the mutations of the C-terminal Ig-like domain or N-glycosylation sites did not affect the association. The association of mouse and human Bsgs, which exhibit high homology in the transmembrane and intracellular domains but low homology in the extracellular domain, was very weak as compared with that within the same species, suggesting the importance of the extracellular domain in the association. If the extracellular domain of the human Ret protein was replaced with the N-terminal Ig-like domain of Bsg, the resulting chimera protein was associated with intact wild-type Bsg, but not if the C-terminal Ig-like domain, instead of the N-terminal one, of Bsg was used. No oligomer formation took place between the intact wild-type Ret and Bsg proteins. In conclusion, these data indicate that the N-terminal Ig-like domain is necessary and sufficient for oligomer formation by Bsg on the plasma membrane.
Microencapsulation of Mono-Dispersed Droplets by Complex Coacervation Method and Membrane Thickness of Generated Capsules. (1997)

マイクロポーラスグラスを用いた膜乳化法によって滴径が良く揃って安定なケロシンエマルションを調整し, このケロシン液滴を芯物質としてゼラチン-アラビアゴム系複合コアセルベーション法によってマイクロカプセルの製作を行った.カプセル化過程での酢酸添加量, 冷却速度, 芯物質添加時期, 更にカプセル被膜硬化過程での水酸化ナトリウム添加量, ホルマリン添加量, 昇温速度の各操作条件が生成マイクロカプセルの膜厚やカプセル内に含有される核数に与える影響を検討した結果, 冷却過程における30から20℃迄の温度領域がカプセル化において極めて重要であること, 低酢酸添加量と低冷却速度が生成カプセルの多核化を防止すること, 硬化過程での操作条件は膜厚, 含有核数のいずれにも大きな影響を与えないことが明らかとなった.さらに, これらの結果は芯物質が固体の場合のカプセル化のデータと比較検討された.
A general prognostic tracking algorithm for predictive maintenance (2002)

Prognostic health management (PHIM) is a technology that uses objective measurements of condition and failure hazard to adaptively optimize a combination of availability, reliability, and total cost of ownership of a particular asset. Prognostic utility for the signature features are determined by transitional failure experiments. Such experiments provide evidence for the failure alert threshold and of the likely advance warning one can expect by tracking the feature(s) continuously. Kalman filters are used to track changes in features like vibration levels, mode frequencies, or other waveform signature features. This information is then functionally associated with load conditions using fuzzy logic and expert human knowledge of the physics and the underlying mechanical systems. Herein is the greatest challenge to engineering. However, it is straightforward to track the progress of relevant features over time using techniques such as Kalman filtering. Using the predicted states, one can then estimate the future failure hazard, probability of survival, and remaining useful life in an automated and objective methodology.
Natural Antibiotic Function of a Human Gastric Mucin Against <i>Helicobacter pylori</i> Infection (2004)

Helicobacter pylori infects the stomachs of nearly a half the human population, yet most infected individuals remain asymptomatic, which suggests that there is a host defense against this bacterium. Because H. pylori is rarely found in deeper portions of the gastric mucosa, where O-glycans are expressed that have terminal alpha1,4-linked N-acetylglucosamine, we tested whether these O-glycans might affect H. pylori growth. Here, we report that these O-glycans have antimicrobial activity against H. pylori, inhibiting its biosynthesis of cholesteryl-alpha-D-glucopyranoside, a major cell wall component. Thus, the unique O-glycans in gastric mucin appeared to function as a natural antibiotic, protecting the host from H. pylori infection.
Multitask Text-to-Visual Embedding with Titles and Clickthrough Data (2019)

Text-visual (or called semantic-visual) embedding is a central problem in vision-language research. It typically involves mapping of an image and a text description to a common feature space through a CNN image encoder and a RNN language encoder. In this paper, we propose a new method for learning text-visual embedding using both image titles and click-through data from an image search engine. We also propose a new triplet loss function by modeling positive awareness of the embedding, and introduce a novel mini-batch-based hard negative sampling approach for better data efficiency in the learning process. Experimental results show that our proposed method outperforms existing methods, and is also effective for real-world text-to-visual retrieval.
Exopolysaccharide biosynthetic glycoside hydrolases can be utilized to disrupt and prevent <i>Pseudomonas aeruginosa</i> biofilms (2016)

Bacterial biofilms present a significant medical challenge because they are recalcitrant to current therapeutic regimes. A key component of biofilm formation in the opportunistic human pathogen Pseudomonas aeruginosa is the biosynthesis of the exopolysaccharides Pel and Psl, which are involved in the formation and maintenance of the structural biofilm scaffold and protection against antimicrobials and host defenses. Given that the glycoside hydrolases PelAh and PslGh encoded in the pel and psl biosynthetic operons, respectively, are utilized for in vivo exopolysaccharide processing, we reasoned that these would provide specificity to target P. aeruginosa biofilms. Evaluating these enzymes as potential therapeutics, we demonstrate that these glycoside hydrolases selectively target and degrade the exopolysaccharide component of the biofilm matrix. PelAh and PslGh inhibit biofilm formation over a 24-hour period with a half maximal effective concentration (EC50) of 69.3 ± 1.2 and 4.1 ± 1.1 nM, respectively, and are capable of disrupting preexisting biofilms in 1 hour with EC50 of 35.7 ± 1.1 and 12.9 ± 1.1 nM, respectively. This treatment was effective against clinical and environmental P. aeruginosa isolates and reduced biofilm biomass by 58 to 94%. These noncytotoxic enzymes potentiated antibiotics because the addition of either enzyme to a sublethal concentration of colistin reduced viable bacterial counts by 2.5 orders of magnitude when used either prophylactically or on established 24-hour biofilms. In addition, PelAh was able to increase neutrophil killing by ~50%. This work illustrates the feasibility and benefits of using bacterial exopolysaccharide biosynthetic glycoside hydrolases to develop novel antibiofilm therapeutics.
Polycrystalline-silicon device technology for large-area electronics (1986)

The process sequence used to fabricate post-hydrogenated polycrystalline silicon thin-film devices has a dramatic impact on performance. A near-optimal process for devices that have hole mobilities of up to 50 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /V . s and electron mobilities of 70 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /V . s is demonstrated. These observed mobilities are substantially higher than previous literature reports. Implantation of boron or phosphorus into the polycrystalline-silicon device channel after the gate-oxidation step allows threshold-voltage tailoring for achievement of either enhancement-or depletion-mode operation of n- and p-channel devices. These results indicate that CMOS or NMOS logic could be fabricated using polycrystalline-silicon devices. Devices with steam-grown gate oxides have reduced channel mobility in comparison with devices oxidized in dry O <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> at the same temperature. Possible mechanisms for the variation in performance with oxidation conditions are discussed.
Antipsychotic-Induced Extrapyramidal Side Effects in Bipolar Disorder and Schizophrenia (2008)

Bipolar patients, especially in depression, were more vulnerable to having acute antipsychotic-induced movement disorders than those with schizophrenia.
Free radicals and myocardial ischemia and reperfusion injury. (1987)

There is a growing body of evidence for the role of free radicals in mediating myocardial tissue injury during myocardial ischemia and in particular during the phase of myocardial reoxygenation. Associated with myocardial ischemia and reperfusion is the generation of oxygen-derived free radicals from a variety of sources that include the mitochondrial electron transport chain; the biosynthesis of prostaglandins; the enzyme xanthine oxidase; and circulating elements in the blood, with the polymorphonuclear neutrophil assuming a primary focus of attention. Experimental studies have shown that free radical scavengers (e.g., N-[2-mercaptopropionyl]glycine) and enzymes that scavenge or degrade reactive species of oxygen (superoxide dismutase or catalase) can reduce the mass of myocardial tissue that undergoes irreversible injury. Additionally allopurinol, which inhibits the enzyme xanthine oxidase, reduces ultimate infarct size, putatively by reducing the xanthine oxidase generation of superoxide anion. Neutrophils that enter the ischemically injured myocardium under the influence of chemotactic attraction and activation of the complement system generate and release highly reactive and cytotoxic oxygen derivatives that are destructive to the vascular endothelium and to the cardiac myocytes. Studies have documented that neutrophil depletion or suppression of neutrophil function (ibuprofen, nafazatrom, BW 755C, or more recently with prostacyclin or iloprost) results in a significant salvage of myocardial tissue that is subjected to a period of regional ischemia followed by reperfusion. Our current understanding of the events associated with myocardial ischemia suggests that within the ischemic myocardial region or area at risk, there is a population of cells that are reversibly injured and that reperfusion within a specified period (less than 3 hours) of time is capable of restoring the majority of the jeopardized cells to a normal status, but that the act of reperfusion itself will lead to the sudden demise of a fraction of the cells because of the cytotoxic effects of reactive species of oxygen derived from one or more of the sources indicated above. The efforts to minimize the amount of tissue that undergoes cell death as a result of myocardial ischemia demand that early reperfusion be established. However, the reintroduction of molecular oxygen and the circulating elements of the blood will be associated with an "explosive" and self-limited destruction of some of the myocardial cells in the area at risk.(ABSTRACT TRUNCATED AT 400 WORDS)
Altered expression of cyclin D1 and CDK4 genes in ovarian carcinomas (1997)

We analyzed the expression and amplification of cyclin D1 and CDK4 genes in ovarian carcinomas. Northern blot analysis revealed overexpression of cyclin D1 in 12 of 65 (18%) ovarian carcinomas while CDK4 was overexpressed in 7 of 48 cases (14%). None of the tumors showed amplification of any of the 2 genes. Overexpression of cyclin D1 and CDK4 transcripts was correlated, suggesting a role of both genes in altered growth control of ovarian cancer cells. Elevated levels of cyclin D1 were significantly associated with a well-moderately differentiated grade (G1-G2) (p < 0.005). No significant association was found between cyclin D1 expression and estrogen receptor, progesterone and epidermal growth factor receptor content. Cyclin D1 expression does not appear to be associated with clinical outcome in human ovarian cancer, although a longer follow-up period and screening of other molecules involved in the same pathway would be necessary to assess this hypothesis. Int. J. Cancer 74:390–395, 1997. © 1997 Wiley-Liss, Inc.
Clinical Data as the Basic Staple of Health Learning: Creating and Protecting a Public Good: Workshop Summary (2011)

1 Front Matter 2 Summary 3 1 Clinical Data as the Basic Staple of the Learning Health System 4 2 U.S. Healthcare Data Today: Current State of Play 5 3 Changing the Terms: Data System Transformation in Progress 6 4 Healthcare Data: Public Good or Private Property? 7 5 Healthcare Data as a Public Good: Privacy and Security 8 6 Creating a Next-Generation Data Utility: Building Blocks and the Action Agenda 9 7 Engaging the Public 10 8 Clinical Data as the Basic Staple of Health Learning: Ideas for Action 11 Appendixes 12 Appendix A: Workshop Agenda 13 Appendix B: Biographical Sketches of Workshop Participants 14 Appendix C: Workshop Attendee List 15 Appendix D: The IOM Committee on Health Research and the Privacy of Health Information: The HIPAA Privacy Rule 16 Other Publications in the Learning Healthcare System Series
An Inductorless Low-Noise Amplifier with Noise Cancellation for UWB Receiver Front-End (2006)

An inductorless low-noise amplifier (LNA) design for ultra-wideband (UWB) receiver front-end is presented. Without on-chip inductors, the ultra-wide bandwidth is achieved by a syncretic adoption of thermal noise canceling, capacitor peaking, and current reuse. Fabricated in a 0.13-μm CMOS technology, the LNA exhibits a small signal gain of 11-dB and a -3-dB bandwidth of 2-9.6-GHz. The input return loss is less than - 9.5-dB, and the noise figure is 3.6-4.8-dB. The LNA consumes 19-mW from a low supply voltage of 1.5-V. The LNA circuit with pad occupies only 0.17 mm2 die area, which is among the smallest reported designs.
Computer-aided diagnosis in chest radiography: a survey (2001)

The traditional chest radiograph is still ubiquitous in clinical practice, and will likely remain so for quite some time. Yet, its interpretation is notoriously difficult. This explains the continued interest in computer-aided diagnosis for chest radiography. The purpose of this survey is to categorize and briefly review the literature on computer analysis of chest images, which comprises over 150 papers published in the last 30 years. Remaining challenges are indicated and some directions for future research are given.
CpGcluster: a distance-based algorithm for CpG-island detection (2006)

CpGcluster uses only integer arithmetic, thus being a fast and computationally efficient algorithm able to predict statistically significant clusters of CpG dinucleotides. Another outstanding feature is that all predicted CGIs start and end with a CpG dinucleotide, which should be appropriate for a genomic feature whose functionality is based precisely on CpG dinucleotides. The only search parameter in CpGcluster is the distance between two consecutive CpGs, in contrast to previous algorithms. Therefore, none of the main statistical properties of CpG islands (neither G+C content, CpG fraction nor length threshold) are needed as search parameters, which may lead to the high specificity and low overlap with spurious Alu elements observed for CpGcluster predictions.
Multiplication by integer constants (1986)

Abstract Methods are given for finding a sequence of ‘add’, ‘subtract’ and ‘shift’ instructions to multiply the contents of a register by an integer constant. Each method generalizes the previous one and requires only a few intermediate or scratch registers. A variation of the last method is used in the PL.8 compiler and uses an unnoticeable amount of the overall compile time. Some statistics roughly indicating the effectiveness of the methods are presented.
New D−π–A-Conjugated Organic Sensitizers Based on 4<i>H</i>-Pyran-4-ylidene Donors for Highly Efficient Dye-Sensitized Solar Cells (2012)

We have synthesized a series of four new promising D-π-A conjugated organic sensitizers with a proaromatic 4H-pyran-4-ylidene as a donor, a thiophene ring in the bridge, and 2-cyanoacrilic acid as acceptor. Comparison between different donor substituents and the modification of the thiophene ring resulted in molar extinction coefficients as high as 36399 M(-1) cm(-1) at 551 nm. The photovoltaic properties of the DSSCs demonstrate power conversion efficiencies as high as 5.4%.
Polycyanurate networks from anethole dimers: Synthesis and characterization (2012)

Abstract Novel biorenewable bisphenols are obtained through simple and rapid chemical transformation of the natural product trans ‐anethole. The corresponding dicyanate esters are thermally cured to give polycyanurate networks. The thermal properties from differential scanning calorimetry, thermogravimetric, and dynamic thermomechanical analyses of the new dicyanate esters compare favorably with similar commercial products. © 2012 Wiley Periodicals, Inc. † J Polym Sci Part A: Polym Chem, 2012