gebhart/patrepeval huggingface dataset:
Thr-1989 Phosphorylation Is a Marker of Active Ataxia Telangiectasia-mutated and Rad3-related (ATR) Kinase (2011)

The DNA damage response kinases ataxia telangiectasia-mutated (ATM), DNA-dependent protein kinase (DNA-PK), and ataxia telangiectasia-mutated and Rad3-related (ATR) signal through multiple pathways to promote genome maintenance. These related kinases share similar methods of regulation, including recruitment to specific nucleic acid structures and association with protein activators. ATM and DNA-PK also are regulated via phosphorylation, which provides a convenient biomarker for their activity. Whether phosphorylation regulates ATR is unknown. Here we identify ATR Thr-1989 as a DNA damage-regulated phosphorylation site. Selective inhibition of ATR prevents Thr-1989 phosphorylation, and phosphorylation requires ATR activation. Cells engineered to express only a non-phosphorylatable T1989A mutant exhibit a modest ATR functional defect. Our results suggest that, like ATM and DNA-PK, phosphorylation regulates ATR, and phospho-peptide specific antibodies to Thr-1989 provide a proximal marker of ATR activation.
A fully-integrated 5 MHz-IF digital FM demodulator (2002)

A 5 MHz-IF digital FM demodulator integrated with a 4th-order bandpass delta-sigma front-end exhibits 74.7 dB SNR, -80.7 dB THD, and 61 dB AM rejection within a 9 kHz message bandwidth. The 0.65 /spl mu/m CMOS chip occupies 3.5 mm/spl times/3.5 mm of active area and consumes 180 mW with 4 V supply and 20 MHz clock.
Learning URL patterns for webpage de-duplication (2010)

Presence of duplicate documents in the World Wide Web adversely affects crawling, indexing and relevance, which are the core building blocks of web search. In this paper, we present a set of techniques to mine rules from URLs and utilize these rules for de-duplication using just URL strings without fetching the content explicitly. Our technique is composed of mining the crawl logs and utilizing clusters of similar pages to extract transformation rules, which are used to normalize URLs belonging to each cluster. Preserving each mined rule for de-duplication is not efficient due to the large number of such rules. We present a machine learning technique to generalize the set of rules, which reduces the resource footprint to be usable at web-scale. The rule extraction techniques are robust against web-site specific URL conventions. We compare the precision and scalability of our approach with recent efforts in using URLs for de-duplication. Experimental results demonstrate that our approach achieves 2 times more reduction in duplicates with only half the rules compared to the most recent previous approach. Scalability of the framework is demonstrated by performing a large scale evaluation on a set of 3 Billion URLs, implemented using the MapReduce framework.
Broadband complex permeability characterization of magnetic thin films using shorted microstrip transmission-line perturbation (2005)

A brief review of the methods used for broadband complex permeability measurement of magnetic thin films up to microwave frequencies is given. In particular, the working principles of the transmission-line perturbation methods for the characterization of magnetic thin films are discussed, with emphasis on short-circuited planar transmission-line perturbation methods. The algorithms for calculating the complex permeability of magnetic thin films for short-circuited planar transmission-line perturbation methods are analyzed. A shorted microstrip line is designed and fabricated as a prototype measurement fixture. The structure of the microstrip fixture and the corresponding measurement procedure are discussed in detail. A piece of 340 nm thick FeTaN thin film deposited on Si substrate using sputtering method is characterized using the microstrip fixture. An improved technique for obtaining permeability by using a saturation magnetization field is demonstrated here, and the results fit well with the Landau–Lifchitz–Gilbert theory. Approaches to extending this method to other aspects in the investigation of magnetic thin film are also discussed.
Lung carcinoma associated with bullous lung disease in young men (1980)

Over a 6 year period, three cases of pulmonary carcinoma in young men with severe bullous lung disease were seen at Washington University Medical Center. The patients did not have a long cigarette-smoking exposure. It would seem that patients with severe bullous lung disease are at a higher risk for the development of pulmonary neoplasm than the general population. Physicians should be aware of this association to expedite diagnosis and therapy.
Ex vivo hepatic gene transfer in mouse using a defective herpes simplex virus-1 vector (1995)

A defective amplicon herpes simplex virus-1 (HSV-1) vector, HSVlac, was used to transfer an E. coli lacZ reporter gene into primary hepatocytes. The lacZ gene was driven by the HSV immediate early (IE) 4/5 promoter. Use of the HSVlac vector resulted in highly efficient gene transfer. Because difficulties in culturing primary hepatocytes impose limitations in ex vivo gene therapy, we sought to determine whether use of the HSVlac vector could simplify gene transfer. Therefore, we incubated HSVlac with primary hepatocytes in suspension and found that the lacZ gene was still transferred with great rapidity and efficiency. To examine lacZ expression in transduced hepatocytes in vivo, we used a mouse hepatocyte transplantation system. In congeneic recipients of primary hepatocytes transduced with HSVlac in suspension, the lacZ gene was expressed in liver and spleen up to 2 weeks. However, survival of transplanted hepatocytes, as well as persistence of HSVlac genome in recipient organs, was demonstrated for up to an 11-week duration of the experiment. These findings suggest that in vivo regulation of the HSV IE4/5 promoter was responsible for the short-term expression of lacZ, which should be overcome by the use of liver-specific promoters. Therefore, our results indicate the feasibility of hepatic gene transfer with a defective HSV-1 vector.
A child's right to die: who should decide? (1992)

When deciding whether to treat children, quality of life is as important as quantity of life. There is some confusion over who has the right to make these treatment decisions. Healthcare professionals are often not the most appropriate decision-makers.
Understanding Points of Correspondence between Sentences for Abstractive Summarization (2020)

Logan Lebanoff, John Muchovej, Franck Dernoncourt, Doo Soon Kim, Lidan Wang, Walter Chang, Fei Liu. Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics: Student Research Workshop. 2020.
Copper(II)-Mediated <i>O</i>-Arylation of Protected Serines and Threonines (2014)

An effective protocol toward the O-arylation of β-hydroxy-α-amino acid substrates serine and threonine has been developed via Chan-Lam cross-coupling. This Cu(II)-catalyzed transformation involves benign open-flask conditions that are well-tolerated with a variety of protected (Boc-, Cbz-, Tr-, and Fmoc-) serine and threonine derivatives and various potassium organotrifluoroborates and boronic acids.
Molecular-targeted therapies in the treatment of squamous cell carcinomas of the head and neck (2008)

Proof of the concept that molecular-targeted therapy is a valid therapeutic approach for head and neck squamous cell carcinoma has emerged with anti-epidermal growth factor receptor agents. Nevertheless, identification of predictive biomarkers of resistance or sensitivity to these therapies remains the main challenge in the optimal selection of patients most likely to benefit from them.
On Statistically Assessing Critical Population Size of an Endangered Species in a Random Environment (1988)

Factors that might influence critical population size in a random environment are considered. The female population is modelled as an age-dependent branching process, in which fertility and mortality depend on an autoregressive process that produces stochastic changes in the environment. Attention was also devoted to methods for utilizing sparse vital statistics in the computer implementation of the model as well as choosing those statistics that summarized a sample of Monte Carlo estimates of critical population size in an informative way. Two extreme values statistics, the Max and Min, and the sample means, computed as functions of time, were used to provide reductions of the data that were judged to be statistically informative. The experiments reported in this paper, using data on chimpanzees, along with those reported elsewhere for other species, indicated that, given two environmental processes with the same variance, the level of uncertainty surrounding mean estimates of critical population size is determined largely by the form of the autocorrelation function of the environmental process. In general, those autocorrelation functions that were strictly positive led to higher levels of uncertainty, as measured by the extreme value statistics, than did those that changed sign.
Fertilization Events Induced by Neurotransmitters After Injection of mRNA in <i>Xenopus</i> Eggs (1988)

Fertilization initiates in the egg a dramatic increase in intracellular calcium that opens ion channels and causes exocytosis. To explore the possibility that these events might involve a receptor-mediated pathway, receptors for serotonin or acetylcholine (M1 muscarinic) were expressed in the Xenopus egg; serotonin or acetylcholine then could initiate a series of responses similar to those normally initiated by sperm. Thus, there may be an endogenous receptor in the egg membrane that is activated by sperm, and the serotonin or M1 muscarinic receptor may replace the sperm receptor in this pathway.
Unstable angina and non-ST-segment elevation myocardial infarction: part I. Initial evaluation and management, and hospital care. (2004)

Each year, more than 1 million patients are admitted to U.S. hospitals because of unstable angina and non-ST-segment elevation myocardial infarction (UA/NSTEMI). To help standardize the assessment and treatment of these patients, the American College of Cardiology and the American Heart Association convened a task force to formulate a management guideline. This guideline, which was published in 2000 and updated in 2002, highlights recent medical advances and is a practical tool to help physicians provide medical care for patients with UA/NSTEMI. Management of suspected UA/NSTEMI has four components: initial evaluation and management; hospital care; coronary revascularization; and hospital discharge and post-hospital care. Part I of this two-part article discusses the first two components of management. During the initial evaluation, the history, physical examination, electrocardiogram, and cardiac biomarkers are used to determine the likelihood that the patient has UA/NSTEMI and to aid in risk assessment when the diagnosis is established. Hospital care consists of appropriate initial triage and monitoring. Medical treatment includes anti-ischemic therapy (oxygen, nitroglycerin, beta blocker), antiplatelet therapy (aspirin, clopidogrel, platelet glycoprotein IIb/IIIa inhibitor), and antithrombotic therapy (heparin, low-molecular-weight heparin).
Current Harmonic Estimation Techniques based on Voltage Measurements in Distribution Networks (2018)

Current harmonics generated by power electronic devices and other nonlinear loads have been a major concern in distribution systems due to quality and efficiency deterioration. To find effective solutions to reduce the level of these current harmonics, their magnitude and phase angle need to be first measured. Adding current sensors is not a practical solution at the system level due to cost and technical concerns. Consequently, a harmonic current estimation method based on only voltage measurement is proposed in this paper. The method can be used in smart power electronics systems to find optimum conditions for current harmonic compensations. Analytical calculations are presented for both single- and multi-unit systems followed by simulation results to confirm the validity of the proposed method.
Use of Chemical Coagulants to Control Fouling Potential for Wastewater Membrane Bioreactor Processes (2007)

Chemical coagulation with ferric chloride, alum, and an organic polymer were used to control the fouling potential of mixed liquors for submerged membrane bioreactor (MBR) processes in treating municipal wastewater. Their filterability was evaluated using a submerged hollow fiber ultrafiltration apparatus operated in constant permeate flux mode. The collected transmembrane pressures over filtration time were used to calculate the membrane fouling rates. The results showed that coagulation pretreatment can reduce fouling rates when MBRs were operated above the critical flux. Even though coagulation with the organic polymer formed larger mixed liquor suspended solids particles and had shorter time-to-filtration than those with ferric chloride and alum, the filterability for membrane filtration were similar, indicating that the membrane fouling in MBR systems was mainly controlled by the concentration of smaller colloidal particles.
Different Immunity Elicited by Recombinant H5N1 Hemagglutinin Proteins Containing Pauci-Mannose, High-Mannose, or Complex Type N-Glycans (2013)

Highly pathogenic avian influenza H5N1 viruses can result in poultry and occasionally in human mortality. A safe and effective H5N1 vaccine is urgently needed to reduce the pandemic potential. Hemagglutinin (HA), a major envelope protein accounting for approximately 80% of spikes in influenza virus, is often used as a major antigen for subunit vaccine development. In this study, we conducted a systematic study of the immune response against influenza virus infection following immunization with recombinant HA proteins expressed in insect (Sf9) cells, insect cells that contain exogenous genes for elaborating N-linked glycans (Mimic) and mammalian cells (CHO). While the antibody titers are higher with the insect cell derived HA proteins, the neutralization and HA inhibition titers are much higher with the mammalian cell produced HA proteins. Recombinant HA proteins containing tri- or tetra-antennary complex, terminally sialylated and asialyated-galactose type N-glycans induced better protective immunity in mice to lethal challenge. The results are highly relevant to issues that should be considered in the production of fragment vaccines.
Do You Know Him? Gaze Dynamics Toward Familiar Faces on a Concealed Information Test (2018)

Can gaze position reveal concealed knowledge? During visual processing, gaze allocation is influenced not only by features of the visual input, but also by previous exposure to objects. However, the dynamics of gaze allocation toward personally familiar items remains unclear, especially in the context of revealing concealed familiarity. When memorizing four pictures of faces on a short term memory task, participants’ gaze was initially directed toward a personally familiar face, followed by a strong avoidance from it. This avoidance was evident even when participants were instructed to conceal their familiarity and direct their gaze equally to all faces. On the other hand, participants were partially able to control the initial preference to fixate on the familiar face. By exploiting these patterns, a machine learning classification algorithm and signal detection analysis revealed impressive detection efficiency estimates, suggesting practical applications of recent theoretical insights from the domains of eye tracking and memory.
The Hippo Pathway, YAP/TAZ, and the Plasma Membrane (2019)

The plasma membrane allows the cell to sense and adapt to changes in the extracellular environment by relaying external inputs via intracellular signaling networks. One central cellular signaling pathway is the Hippo pathway, which regulates homeostasis and plays chief roles in carcinogenesis and regenerative processes. Recent studies have found that mechanical stimuli and diffusible chemical components can regulate the Hippo pathway primarily through receptors embedded in the plasma membrane. Morphologically defined structures within the plasma membrane, such as cellular junctions, focal adhesions, primary cilia, caveolae, clathrin-coated pits, and plaques play additional key roles. Here, we discuss recent evidence highlighting the importance of these specialized plasma membrane domains in cellular feedback via the Hippo pathway.
Error-burst detection with tandem CRCs (1991)

The authors investigate the efficacy of using two different cyclic redundancy check (CRC) codes in tandem to increase error-burst detecting capability. For a set of pairs of CRCs which are used in standards, it is found that the guaranteed detectable burst length is less than the sum of the individual guaranteed detectable burst lengths, but not much less. Thus strengthened CRC codes can readily be obtained using existing devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Target material pathways model for high power pulsed magnetron sputtering (2005)

The potential of high power pulsed magnetron sputtering (HPPMS) has created growing interest, because it can generate a dense plasma with high target material ion content. However, reported deposition rates are significantly lower than for dc or midfrequency ac sputtering at the same average power in most cases. The fraction of target material arriving at the workpiece, which is ionized, ranges from 5% to 70% as reported so far by workers in the field, even though optical emission spectroscopy suggests a highly metallic plasma. A simple pathways model has been developed to explain these experimental results. In addition, evaluation of the model for various interesting materials suggests target material characteristics which are desirable in order to achieve higher deposition rates and a greater ionized fraction of target material reaching the substrate. The model will be presented, with representative characteristic results and implications on HPPMS processes. In addition, insights from approximate model equations will be presented.
Shape-controlled, high fill-factor microlens arrays fabricated by a 3D diffuser lithography and plastic replication method (2004)

This paper describes a simple and effective method to fabricate a plastic microlens array with controllable shape and high fill-factor, which utilizes the conventional lithography and plastic replication. The only difference from conventional lithography is the insertion of a diffuser that randomizes paths of the incident ultraviolet (UV) light to form lens-like 3D latent image in a thick positive photoresist. After replication of the developed concave microlens mold onto the polydimethylsiloxane (PDMS), the focal length of the fabricated hemispherical microlens was observed to be 13-88 microm depending on the UV exposure dose. Two PDMS curing conditions were tested, where the elevated temperature of 85 masculineC resulted in smoother surface roughness of 2.6 nm in RMS value in the microlens mold. The proposed method can be extensively applied for microlens fabrication with other plastic materials due to its simplicity and versatility.
WSPeer - An Interface to Web Service Hosting and Invocation (2005)

This paper introduces WSPeer, a high level interface to hosting and invoking Web services. WSPeer aims to support the diversification of Web service deployments by providing a pluggable architecture that can be used to host Web services in a number of different ways. In particular, we are interested in the cross-fertilisation between Web services and peer-to-peer (P2P) systems by enabling entities to act as both service providers and consumers in a flexible and extensible way. Further, we support the behaviour needed within a P2P environment by allowing Web services to be dynamically deployed through the use of a lightweight container that is more suited to highly transient connectivity. This approach allows standard Web services to be deployed within a P2P environment and yet still adhere to a service oriented architecture. We argue therefore that both Web services and P2P are exponents of service oriented architecture, approaching the same goals from very different directions, and that a combination of the strengths of these approaches can lead to more robust and ubiquitous Web service and P2P deployments.
Induced Pluripotent Stem Cells Generate Both Retinal Ganglion Cells and Photoreceptors: Therapeutic Implications in Degenerative Changes in Glaucoma and Age-Related Macular Degeneration (2010)

The direct reprogramming of somatic cells to a pluripotent state holds significant implications for treating intractable degenerative diseases by ex vivo cell therapy. In addition, the reprogrammed cells can serve as a model for diseases and the discovery of drugs and genes. Here, we demonstrate that mouse fibroblast induced pluripotent stem cells (iPSCs) represent a renewable and robust source of retinal progenitors, capable of generating a wide range of retinal cell types that includes retinal ganglion cells (RGCs), cone, and rod photoreceptors. They respond to simulated microenvironment of early and late retinal histogenesis by differentiating into stage-specific retinal cell types through the recruitment of normal mechanisms. The depth of the retinal potential of iPSCs suggests that they may be used to formulate stem cell approaches to understand and treat a wide range of retinal degenerative diseases from glaucoma to age-related macular degeneration (AMD).
Fabrication of wafer level chip scale packaging for optoelectronic devices (2003)

A novel, simple processing and wafer level packaging method for a 4/spl times/4 Resonant Cavity LEDs chip with individual array is under development. Palladium/Gold (Pd/Au) alloys are used as p-type contacts and as rewiring metallization for optoelectronic devices to improve the fabrication process. By use of these alloys we have found a reduction of a factor of 10 in the resistance compared to Titanium/Gold (Ti/Au), due to the formation of a conducting oxide at the interface between the metal and semiconductor. On the packaging side, electroplated solder deposition was used to fabricate eutectic solderbump arrays on the chip. For the Under Bump Metallurgies (UBM), a thin layer (100 nm) of Ti and a layer (200 nm) of Cu was sputtered on the wafer. A 10 /spl mu/m thick copper stud is platted on top of the UBM to be used as a stem for the solder.
Towards Real Time Team Optimization (2019)

Teams can be often viewed as a dynamic system where the team configuration evolves over time (e.g., new members join the team; existing members leave the team; the skills of the members improve over time). Consequently, the performance of the team might be changing due to such team dynamics. A natural question is how to plan the (re-)staffing actions (e.g., recruiting a new team member) at each time step so as to maximize the expected cumulative performance of the team. In this paper, we address the problem of real-time team optimization by intelligently selecting the best candidates towards increasing the similarity between the current team and the high-performance teams according to the team configuration at each time-step. The key idea is to formulate it as a Markov Decision process (MDP) problem and leverage recent advances in reinforcement learning to optimize the team dynamically. The proposed method bears two main advantages, including (1) dynamics, being able to model the dynamics of the team to optimize the initial team towards the direction of a high-performance team via performance feedback; (2) efficacy, being able to handle the large state/action space via deep reinforcement learning based value estimation. We demonstrate the effectiveness of the proposed method through extensive empirical evaluations.