gebhart/patrepeval huggingface dataset:
A small nucleolar RNA:ribozyme hybrid cleaves a nucleolar RNA target <i>in vivo</i> with near-perfect efficiency (1999)

A hammerhead ribozyme has been localized to the yeast nucleolus by using the U3 small nucleolar RNA as a carrier. The hybrid small nucleolar RNA:ribozyme, designated a "snorbozyme," is metabolically stable and cleaves a target U3 RNA with nearly 100% efficiency in vivo. This is the most efficient in vivo cleavage reported for a trans-acting ribozyme. A key advantage of the model substrate featured is that a stable, trimmed cleavage product accumulates. This property allows accurate kinetic measurements of authentic cleavage in vivo. The system offers new avenues for developing effective ribozymes for research and therapeutic applications.
Computer assisted coronary intervention: 3D reconstruction and determination of optimal views (2002)

The authors propose a novel method for computer assisted coronary intervention. The 3D coronary arterial tree is first reconstructed based on a pair of angiograms acquired from single-plane or bi-plane systems at arbitrary orientations. With this 3D structure, the views of selected vessel segments with minimal vessel foreshortening and overlapping are determined in the form of a sequence of gantry angulations. A computer simulation confirmed the accuracy of 3D centerline reconstruction to within 2.5% error. To date 3D reconstruction have been completed in 20 RCA, 16 LCA, and 3 bypass grafts. With the proposed technique, coronary sizing can be optimized for lesion length. Practice interventions can be completed in this computer assisted process that should lead to more accurate, efficient, and safe coronary procedure.
Anti-idiotypic antibody Ab2/3H6 mimics the epitope of the neutralizing anti-HIV-1 monoclonal antibody 2F5 (2002)

Anti-idiotypic antibodies directed against potentially neutralizing anti-HIV-1 antibodies may mimic epitopes on gp41 otherwise cryptic to the immune system. This study reports the generation of murine monoclonal antibody Ab2/3H6 blocking the binding of human Ab1 2F5 to the synthetic epitope and to gp160 in an enzyme-linked immunosorbent competition assay. Ab2/2H6 diminished the neutralizing potency of 2F5 in an in-vitro neutralization assay. Ab2/3H6 Fab fragments were capable of inducing neutralizing immune and 2F5-specific responses in B6D2F1 mice applying a simple prime-boost regimen of immunization.
Optical Communications Using Light Beams Carrying Orbital Angular Momentum (2012)

We described recent progress on optical communications using light beams carrying orbital angular momentum (OAM). We achieved a 25.6-bit/s/Hz spectral efficiency using 16-QAM signals over pol-muxed four OAM beams. We obtained a 2-Tbit/s data link using 25-WDM-channel 40-Gbit/s NRZ-DPSK signals over two OAM beams.
<title>Evaluation of an automated segmentation method based on performances of an automated classification method</title> (2000)

We have developed a computerized method for the automatic segmentation of mass lesions on digitized mammograms using gray-level region-growing. This segmentation technique has been incorporated into our automated classification scheme which consists of (1) automated segmentation (2) automated feature-extraction and (3) determination of likelihood of malignancy using an automated classifier. The feature- extraction techniques extract various features from the neighborhoods of the computer-grown mass region to characterize the margin, shape and density of the mass. The automated classifier is then used to merge these computer- extracted features into a number related to the likelihood of malignancy. To evaluate quantitatively the performance of the segmentation technique, we calculate the area of overlap between the computer-grown mass regions and radiologist- identified mass regions. In addition, we substitute the computer-identified margins with radiologist-identified margins in our classification scheme. The performances of individual features as well as the classification scheme in terms of their ability to differentiate between benign and malignant masses are evaluated using receiver operating characteristic (ROC) analysis. The performance obtained based on the mass regions identified by the automated segmentation technique and by radiologists are compared to evaluate the adequacy of the region growing. Results from this study show that the automated segmentation technique tends to undergrow the mass regions by approximately one quarter of the area identified by the radiologists. However, the superior performances of the computer-extracted features and the classification scheme based on the analysis of the computer- grown mass regions indicated that the computer-grown mass regions are sufficient for the subsequent techniques of feature-extraction and classification to accurately characterize mass lesions.
A fast magnetoelectric device based on current-driven domain wall propagation (2016)

Several emerging spintronic devices have recently been proposed, performing computation by (a) generating spin currents based on input magnet states to switch an output magnet state using Spin-Transfer Torque (STT) [1,2], (b) using multiple nanopillars to drive a domain wall (DW) that switches an output nanopillar using STT [7], and (c) using magnetoelectric (ME) switching at the input, combined with DW automotion, to switch an output state [3]. All of these devices have delays of several nanoseconds. The energy for (a) and (b) is in the range of femtoJoules, while the ME mechanism in (c) facilitates greater energy-efficiency, in the aJ range. These numbers fall some distance away from CMOS, where gate delays and switching energies are in the range of picoseconds (ps) and attoJoules (aJ), respectively.
Characterization of Primary Standards for Use in the HPLC Analysis of the Procyanidin Content of Cocoa and Chocolate Containing Products (2009)

This report describes the characterization of a series of commercially available procyanidin standards ranging from dimers DP = 2 to decamers DP = 10 for the determination of procyanidins from cocoa and chocolate. Using a combination of HPLC with fluorescence detection and MALDI-TOF mass spectrometry, the purity of each standard was determined and these data were used to determine relative response factors. These response factors were compared with other response factors obtained from published methods. Data comparing the procyanidin analysis of a commercially available US dark chocolate calculated using each of the calibration methods indicates divergent results and demonstrate that previous methods may significantly underreport the procyanidins in cocoa-containing products. These results have far reaching implications because the previous calibration methods have been used to develop data for a variety of scientific reports, including food databases and clinical studies.
Electrochemical Formation of Stable p-i-n Junction in Conjugated Polymer Thin Films (2009)

Stable p-i-n junction was formed in polymer thin films by a facile electrochemical method. The polymer thin films contained an alkoxyphenyl substituted poly(1,4-phenylene vinylene), a cross-linkable liquid trimethylolpropane trimethacrylate (TMPTMA), and lithium trifluoromethane sulfonate at a weight ratio of 20:10:1. The thin films were sandwiched between an indium tin oxide anode and an aluminum cathode. During initial charging at 12 V, a p-i-n junction was formed in a similar fashion as reported in the polymer light-emitting electrochemical cells except that the junction did not relax during subsequent idling without external bias. TMPTMA was responsible in conducting the ions (dopants) during the formation of the junction. The junction stabilized as TMPTMA cured and lost its ionic conductivity. This mechanism is supported by the measurements of the electroluminescence behavior, the photovoltaic response and the AC impedance of the charged devices. The formation of the stable p-i-n junction improves the electroluminescence performance and photovoltaic efficiency compared to similar devices without such a junction. The polymer p-i-n junction devices exhibited current-voltage response characteristic of light-emitting diodes with turn-on time<5 mS. The luminance efficiency was 3.0 cd/A, and brightness was 450 Cd/m2 at 10 V. The same junction devices under 100 mW/cm(-2) AM1.5 solar illumination had an open-circuit voltage of 1.5 V and a short circuit current of 6 microA/cm2 with an over 460% enhancement on efficiency compared to the device without the junction.
Combining one‐step Sanger sequencing with phasing probe hybridization for HLA class I typing yields rapid, G‐group resolution predicting 99% of unique full length protein sequences (2017)

Our combined method routinely provides biologically relevant typing resolution at the level of the ARD. It can be applied to both single samples or to large volume typing supporting either bone marrow or solid organ transplantation using technologies currently available in many HLA laboratories.
Neuropathic pain due to chronic idiopathic axonal neuropathy: fast pain reduction after topical phenytoin cream application (2018)

Pain due to chronic idiopathic axonal polyneuropathy (CIAP) is often treated with therapies based on general neuropathic pain guidelines, which are mainly developed with randomized clinical trials having valuated treatments for painful diabetic neuropathy (PDN) and post-herpetic neuralgia. No clinical trial studying treatments for patients with painful CIAP has been yet executed, thus only extrapolation of the value of treatments from other neuropathic pain fi elds is possible. Clearly, the pathogenesis and pathophysiology of CIAP will be quite different from that of PDN. Many CIAP patients complain of intolerable side effects of current analgesic medication. In order to help those patients, we developed a treatment-regime consisting of the supplement palmitoylethanolamide and topical formulations of analgesics. This combination is rarely complicated by side effects. One of our most recent topical formulation we developed contains 10% phenytoin, a broad acting voltage-gated sodium-channel blocker. Phenytoin 10% cream can also be used as a stand-alone therapy as we will discuss.
Robust Monitoring of Link Delays and Faults in IP Networks (2006)

In this paper, we develop failure-resilient techniques for monitoring link delays and faults in a Service Provider or Enterprise IP network. Our two-phased approach attempts to minimize both the monitoring infrastructure costs as well as the additional traffic due to probe messages. In the first phase, we compute the locations of a minimal set of monitoring stations such that all network links are covered, even in the presence of several link failures. Subsequently, in the second phase, we compute a minimal set of probe messages that are transmitted by the stations to measure link delays and isolate network faults. We show that both the station selection problem as well as the probe assignment problem are NP-hard. We then propose greedy approximation algorithms that achieve a logarithmic approximation factor for the station selection problem and a constant factor for the probe assignment problem. These approximation ratios are provably very close to the best possible bounds for any algorithm
Matching reviews to objects using a language model (2009)

We develop a general method to match unstructured text reviews to a structured list of objects. For this, we propose a language model for generating reviews that incorporates a description of objects and a generic review language model. This mixture model gives us a principled method to find, given a review, the object most likely to be the topic of the review. Extensive experiments and analysis on reviews from Yelp show that our language model-based method vastly outperforms traditional tf-idf-based methods.
Precisely-controlled DNA-templated micelle as a multifunctional delivery platform for glioblastoma therapeutics (2016)

Frontiers Events is a rapidly growing calendar management system dedicated to the scheduling of academic events. This includes announcements and invitations, participant listings and search functionality, abstract handling and publication, related events and post-event exchanges. Whether an organizer or participant, make your event a Frontiers Event!
OPTIMAL CONTROL THEORY APPLIED TO A DIFFERENCE EQUATION MODEL FOR CARDIOPULMONARY RESUSCITATION (2005)

The techniques of optimal control are applied to a validated blood circulation model of cardiopulmonary resuscitation (CPR), consisting of a system of seven difference equations. In this system, the nonhomogeneous forcing term is the externally applied chest pressure acting as the "control". We seek to maximize the blood flow, as measured by the pressure differences between the thoracic aorta and the superior vena cava. The new aspect in this application is that the control values from the two previous time steps are used to calculate the pressures (state variables) at the current time step. We prove the existence and uniqueness of the optimal control and provide a new CPR strategy, with increased blood flow. The characterization of the optimal control is given in terms of the solutions of the circulation model and of the corresponding adjoint system. The numerical results show a significant increase in the blood flow as compared with standard CPR.
On the Function of the 14 Å Long Internal Cavity of Histone Deacetylase-Like Protein:  Implications for the Design of Histone Deacetylase Inhibitors (2004)

Histone deacetylases (HDACs) play an important role in gene transcription. Inhibitors of HDACs induce cell differentiation and suppress cell proliferation in tumor cells. AutoDock calculations of known and novel HDAC inhibitors as well as of several probe molecules to histone deacetylase-like protein (HDLP), using a modified scoring function for metalloproteins, demonstrate excellent agreement (R = 0.92) between experimental and computed binding constants. Analysis of the docked structures allows a determination of the different binding motifs in known inhibitors. Such calculations are a useful tool for the prediction of binding constants for new HDAC inhibitors. Exploration of the 14 A long internal cavity adjacent to the active site by docking of small molecular probes suggest that it plays a crucial role by accepting the cleaved acetate and releasing it at the far side of the cavity. The importance of the findings for the design of new inhibitors is discussed.
Sensing vehicle dynamics for determining driver phone use (2013)

This paper utilizes smartphone sensing of vehicle dynamics to determine driver phone use, which can facilitate many traffic safety applications. Our system uses embedded sensors in smartphones, i.e., accelerometers and gyroscopes, to capture differences in centripetal acceleration due to vehicle dynamics. These differences combined with angular speed can determine whether the phone is on the left or right side of the vehicle. Our low infrastructure approach is flexible with different turn sizes and driving speeds. Extensive experiments conducted with two vehicles in two different cities demonstrate that our system is robust to real driving environments. Despite noisy sensor readings from smartphones, our approach can achieve a classification accuracy of over $90\%$ with a false positive rate of a few percent. We also find that by combining sensing results in a few turns, we can achieve better accuracy (e.g., $95\%$) with a lower false positive rate.
Flow chamber and microfluidic approaches for measuring thrombus formation in genetic bleeding disorders (2017)

Platelet adhesion and aggregation, coagulation, fibrin formation, and fibrinolysis are regulated by the forces and flows imposed by blood at the site of a vascular injury. Flow chambers designed to observe these events are an indispensable part of doing hemostasis and thrombosis research, especially with human blood. Microfluidic methods have provided the flexibility to design flow chambers with complex geometries and features that more closely mimic the anatomy and physiology of blood vessels. Additionally, microfluidic systems with integrated optics and/or pressure sensors and on-board signal processing could transform what have been primarily research tools into clinical assays. Here, we describe a historical review of how flow-based approaches have informed biophysical mechanisms in genetic bleeding disorders, challenges and potential solutions for developing models of bleeding in vitro, and outstanding issues that need to be addressed prior to their use in clinical settings.
The sonic Doppler flowmeter (1980)

Industrial applications of the Doppler principle to flow measurement have recently increased in acceptance. Reasonably accurate measurements have been limited to turbulent flow conditions. In the Argonne Doppler flowmeter, as in most commercial units, ultrasonic energy (either in cw or tone burst form) is transmitted at an angle through the pipe wall, and sound backscattered from particles or bubbles, is detected by a second transducer. The Doppler frequency difference between received and transmitted signal is obtained by subtraction. This is a noise of finite bandwidth. For turbulent flow the bandwidth is small enough to permit simple techniques such as counting or frequency to voltage conversion to serve as the Doppler shift indicator with a scale factor close to unity. For laminar flow, a band limited fiat Doppler spectrum is predicted and observed, with the cutoff frequency at twice the predicted Doppler shift. Measurement of such a spectrum is automated with servo controlled adjustable filters. This technique opens up the possibility of using the Doppler method on high viscosity slurries.
Functional cache chip for improved system performance (1989)

The use of a cache to improve the performance of computing systems is becoming very pervasive, from microprocessors to high-end systems. The general approach has traditionally been to use ordinary fast RAM chips and interface these close to the processor for speed. However, this is far from the ideal solution. The stringent and often conflicting requirements on the cache bandwidth for servicing the processor and minimizing reload time can severely limit attainable performance. The cache need not be the performance-limiting factor if a properly integrated functional cache chip is used. This paper defines the basic requirements of a cache subsystem and shows how these have been or could be implemented in typical systems. Subsequently, the functional requirements of an optimal cache chip design are presented and illustrated.
Mechanism of Bacterial Oligosaccharyltransferase (2013)

N-Linked glycosylation is an essential post-translational protein modification in the eukaryotic cell. The initial transfer of an oligosaccharide from a lipid carrier onto asparagine residues within a consensus sequon is catalyzed by oligosaccharyltransferase (OST). The first X-ray structure of a complete bacterial OST enzyme, Campylobacter lari PglB, was recently determined. To understand the mechanism of PglB, we have quantified sequon binding and glycosylation turnover in vitro using purified enzyme and fluorescently labeled, synthetic peptide substrates. Using fluorescence anisotropy, we determined a dissociation constant of 1.0 μm and a strict requirement for divalent metal ions for consensus (DQNAT) sequon binding. Using in-gel fluorescence detection, we quantified exceedingly low glycosylation rates that remained undetected using in vivo assays. We found that an alanine in the -2 sequon position, converting the bacterial sequon to a eukaryotic one, resulted in strongly lowered sequon binding, with in vitro turnover reduced 50,000-fold. A threonine is preferred over serine in the +2 sequon position, reflected by a 4-fold higher affinity and a 1.2-fold higher glycosylation rate. The interaction of the +2 sequon position with PglB is modulated by isoleucine 572. Our study demonstrates an intricate interplay of peptide and metal binding as the first step of protein N-glycosylation.
Efficacy of Bordetella bronchiseptica Bacterin in Controlling Enzootic Atrophic Rhinitis in Swine (1979)

The efficacy of a Bordetella bronchiseptica bacterin was evaluated in 2 commercial swine herds affected with mild and severe enzootic atrophic rhinitis (AR). In the 1st herd study, (mild AR), the degree of clinical AR, nasal turbinate evaluation, blood serum titer to B bronchiseptica antigen, and adjusted days from birth to 100 kg were determined for individual pigs. Bacterin inoculation reduced the incidence and severity of gross turbinate atrophy 57% and reduced clinical AR over 93%. Inoculated swine had an average blood serum-agglutinating titer greater than 1:2,793 and noninoculated (control) swine had an average titer of 1:112. Increased serum titer significantly (P less than 0.05) correlated with decreased degree of nasal turbinate atrophy. Inoculated and control pigs reached 100 kg in an average of 171 and 178 days after birth, respectively. In the 2nd study (severe enzootic AR), inoculated and control pigs were individually evaluated for clinical AR and total average daily weight gain. Inoculation reduced clinical AR over 90%. The total average daily gain for the inoculated and control pits was 435.84 g and 340.50 g, respectively. Inoculated pigs and control pigs reached 100-kg market weight in 184 and 238 days, respectively.
Generating Queries with Cardinality Constraints for DBMS Testing (2006)

Good testing coverage of novel database techniques, such as multidimensional histograms or changes in the execution engine, is a complex problem. In this work, we argue that this task requires generating query instances, not randomly, but based on a given set of constraints. Specifically, obtaining query instances that satisfy cardinality constraints on their subexpressions is an important challenge. We show that this problem is inherently hard, and develop heuristics that effectively find approximate solutions
Single station ocean current vector measurement: Application of the Spaced Antenna (SA) Technique (1989)

The Spaced Antenna (SA) technique is applied to measuring ocean surface currents for the first time. This allows the measurement of the ocean surface current transverse to the radar beam as well as the radial current and thus eliminates the requirement of two separate radars to measure the full current vector as with present ocean surface current radar systems. Therefore, this technique offers considerable advantages for ocean current mapping in terms of simplicity for real‐time operational systems and could have wide applications, for example at sites where it is not practical to have two separate radars.
Position control methods of spherical ultrasonic motor (2010)

In this paper, we investigate the position control of spherical ultrasonic motor (SUSM). The generated torque of SUSM is influenced by the phase difference and the driving frequency of applied AC voltages. Therefore, the control strategy is classified into three types: (a) variable phase and fixed frequency, (b) fixed phase and variable frequency, and (c) variable phase and frequency. We formulate the position control rules for SUSM based on the above three types of control variables, and investigate the performances experimentally.