gebhart/patrepeval huggingface dataset:
Validation of the IHC4 Breast Cancer Prognostic Algorithm Using Multiple Approaches on the Multinational TEAM Clinical Trial (2015)

The use of the IHC4 algorithm was validated on the TEAM trial for predicting residual risk in patients with breast cancer. These data support the use of the IHC4 algorithm clinically, but quantitative and standardized approaches need to be used.
Magnetic Anchored and Cable Driven Endoscope for Minimally Invasive Surgery (2023)

Globally, the minimally invasive surgery (MIS) has been applied to more and more medical fields. MIS can provide many benefits for the patient, such as reduced pain, faster recovery, and better cosmesis [1]. But it also causes many challenges to the doctor and assistant during the long surgery. The most prominent problem is how to get the desired view through the narrow incision and the current solution is to insert a rigid endoscope into the surgical cavity of the patient. But this method will also bring about many problems and magnify the difficulty of the surgery. Firstly, the motion of the endoscope is limited by the incision especially when sharing the same port with other instruments, leading to the insufficient field of view (FOV) during the surgery. Also, the frequent collisions between the endoscope and other instruments will also interfere the adjustment of FOV. To address the above issues, the magnetic anchored and guided system (MAGS) is proposed [2]. Due to there is no rigid shaft and the endoscope is attached on the inner wall of the surgical cavity, the problems of port-crowing and instrument-fencing can be significantly alleviated, as shown in Fig.1. But how to arrange and control additional degrees of freedom (DOF) on MAGS to make it can cover the full FOV for surgeon is still a challenging problem. Here, we introduce the cable-driven mechanism to combine with the magnetic actuation method, providing a feasible solution for clinical application.
Exploiting Conformationally Constrained Peptidomimetics and an Efficient Human-Compatible Delivery System in Synthetic Vaccine Design (2002)

In the communication by J. A. Robinson, G. Pluschke, and co-workers in Issue 11, 2001, pp. 838–843, the structures of peptidomimetics 2 and 5 were incorrect. The correct structures are shown below. The mimetics 1 and 4 were coupled through a β-alanine linker to a regioisomer of phosphatidylethanolamine (PE′, rac-1-palmitoyl-3-oleoyl-phosphatidylethanolamine), to afford the conjugates 2 and 5, ready for incorporation into immunopotentiating reconstituted influenza virosomes (IRIVs). The conclusions of the work are not altered by the incorrect structures.1
Reactions of 2,3‐diamino‐4(3<i>H</i>)‐pyrimidinones. II (1985)

Abstract The reaction of 2,3‐diamino‐4(3 H )‐pyrimidinones with α,β‐diketones and orthoesters is described.
Information-Based Sequential Selection of Clinical Tests in Risk Assessment (2012)

We present a new framework for supporting decisions in sequential clinical risk assessment examinations. In this framework, the decision whether to perform a test depends on its expected contribution to risk assessment, given results of previous tests, and the contribution is quantified using information theory. In many cases adding an additional examination clearly improves the predictive model. However, there are cases in which the improvement is not constant for all values of previous tests, and quantification of possible improvement can support decision on further examinations. Using this approach can prevent many expensive, unpleasant or risky examinations. We demonstrate the use of this method on an example of type 2 diabetes onset study. The results show that reducing a considerable percent of the blood tests does not decrease the model's prediction power.
Auto-calibration of cylindrical multi-projector systems (2010)

In this paper we present a novel technique to calibrate multiple casually aligned projectors on a fiducial-free cylindrical curved surface using a single camera. We impose two priors to the cylindrical display: (a) cylinder is a vertically extruded surface; and (b) the aspect ratio of the rectangle formed by the four corners of the screen is known. Using these priors, we can estimate the display's 3D surface geometry and camera extrinsic parameters using a single image without any explicit display to camera correspondences. Using the estimated camera and display properties, we design a novel deterministic algorithm to recover the intrinsic and extrinsic parameters of each projector using a single projected pattern seen by the camera which is then used to register the images on the display from any arbitrary viewpoint making it appropriate for virtual reality systems. Finally, our method can be extended easily to handle sharp corners - making it suitable for the common CAVE like VR setup. To the best of our knowledge, this is the first method that can achieve accurate geometric auto-calibration of multiple projectors on a cylindrical display without performing an extensive stereo reconstruction.
Ultrasound-Guided HIFU Neurolysis Of Peripheral Nerves to Treat Spasticity and Pain (2005)

Spasticity, a major complication of disorders of the central nervous system (CNS) signified by uncontrollable muscle contractions, is difficult to treat effectively. We report on the use of image‐guided high‐intensity focused ultrasound (HIFU) to target and suppress the function of the sciatic nerve complex of rabbits in vivo as a possible treatment of spasticity and pain. In situ focal acoustic intensity of 1480–1850 W/cm2 was applied using a scanning method. HIFU treatment of 36 ± 14 s (mean ± standard deviation) was effective in achieving complete conduction block in 100% of the 22 nerves treated (11 rabbits). Histological examination indicated axonal demyelination as a probable mechanism of nerve block.
Method and apparatus for determining relative phase and sensitivity of elements in an acoustic array (1979)

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Intumescent coatings based on 4,4 prime-dinitrosulfanilide (1977)

Nitroaromatic amine-based intumescent coatings which offer improved thermal protection to a substrate by reducing the backface temperature rise have been developed. The intumescent monomer agent is 4,4 prime-dinitrosulfanilide. This agent has an intumescent temperature of 220 deg C, compared with 300 deg C for the ammonium salt of 1,4-nitroaniline-2-sulfonic acid and offers a twelve-fold reduction in water solubility over this compound. On the basis of differential thermal analysis and screening tests, a chlorinated polyolifin epoxy-reactive butadiene acrylonitrile rubber blend was selected as a flame quenching binder.
A frequency-domain approach to crosstalk identification in xDSL systems (2001)

Crosstalk between multiple services transmitting through the same telephone cable is the primary limitation to digital subscriber line services. From a spectrum management point of view, it is important to have an accurate map of all the services that generate crosstalk into a given pair. If crosstalk is measured via modem-based methods, i.e., while a digital subscriber line (DSL) system is running, what is measured is the crosstalk in the bandwidth of the considered DSL system. For this reason, DSL services running on adjacent pairs may not be detected if their bandwidth is not significantly overlapping with the bandwidth of the disturbed system. This is a major drawback of modem-based system identification techniques since, from a spectrum management point of view, it is important to be able to identify all crosstalkers. We address the important problem of crosstalk identification when the pair under test does not bear DSL services, i.e., via a non-modem-based approach. Crosstalk sources are identified in the frequency domain by finding the maximum correlation with a "basis set" of representative measured crosstalk couplings. The effectiveness of the proposed technique is also verified on the basis of real crosstalk measurements performed on actual cables. Finally, new techniques based on multiple regression and best basis selection are also discussed.
Sulfation of sialyl lactosamine oligosaccharides by chondroitin 6-sulfotransferase (1997)

We have previously shown that chondroitin 6-sulfotransferase (C6ST) catalyzes transfer of sulfate not only to position 6 of GalNAc residue of chondroitin but also to position 6 of Gal residue of keratan sulfate. In this study, we examined the sulfation of sialyl lactosamine oligosaccharides by C6ST. C6ST catalyzed transfer of sulfate to NeuAc alpha 2-3Gal beta 1-4GlcNAc (SLN), NeuAc alpha 2-3Gal beta 1-4GlcNAc beta 1-3Gal beta 1-4GlcNAc (SL1L1), NeuAc alpha 2-3Gal beta 1-4(6-sulfo)GlcNAc beta 1-3(6-sulfo)Gal beta 1-4(6-sulfo)GlcNAc (SL2L4), and their desialylated derivatives, but not to NeuAc alpha 2-3Gal beta 1-4(Fuc alpha 1-3)GlcNAc (SLe(x)). The sulfated product formed from SLN was degraded with neuraminidase and reduced with NaBH4. The resulting sulfated disaccharide alditol showed the same retention time in SAX-HPLC as that of [3H]Gal(6SO4) beta 1-4GlcNAc-ol. The sulfated product formed from SLN was also degraded by a reaction sequence of neuraminidase digestion, hydrazinolysis, deamination, and NaBH4 reduction. The final product was coeluted with [3H]Gal(6SO4) beta 1-4anhydromannitol in SAX-HPLC. These observations show that C6ST could transfer sulfate to position 6 of Gal residue of SLN. Incorporation of sulfate into SL2L4 was much higher than the incorporation into SL1L1, suggesting that sulfate moiety attached to adjacent GlcNAc residue may stimulate the transfer of sulfate to Gal residue. The recombinant C6ST also catalyzed sulfation of the sialyl lactosamine oligosaccharides, indicating that a single protein catalyzes sulfation of chondroitin, keratan sulfate, and sialyl lactosamine oligosaccharides. These results raised a possibility that C6ST may be one of the candidates involved in the biosynthesis of sulfated sialyl Lewis x ligand for L-selectin.
Lytic activity of the virion-associated peptidoglycan hydrolase HydH5 of Staphylococcus aureusbacteriophage vB_SauS-phiIPLA88 (2011)

The virion-associated PG hydrolase HydH5 has lytic activity against S. aureus, which makes it attractive as antimicrobial for food biopreservation and anti-staphylococcal therapy.
Geometries for streamflow measurement using a UHF RiverSonde (2004)

Three geometries for a UHF streamflow radar system are examined: bistatic across the channel, monostatic on a bank, and monostatic in the center of the channel. The radar operates by analyzing the frequency spectrum of the received energy and determining the angles of arrival of energy at each frequency, so it is important to understand how the various geometries affect the width of the frequency spectrum and its angular distribution. We argue that placing the radar and antenna on one bank, with the antennas looking broadly across the river, generally produces the best results. The broad frequency spectrum allows many points to be analyzed, most of which have single-angle direction solutions (which generally are more robust than dual-angle solutions), and all the equipment can be placed at a single location.
Characterizing typical and atypical user sessions in clickstreams (2008)

Millions of users retrieve information from the Internet using search engines. Mining these user sessions can provide valuable information about the quality of user experience and the perceived quality of search results. Often search engines rely on accurate estimates of Click Through Rate (CTR) to evaluate the quality of user experience. The vast heterogeneity in the user population and presence of automated software programs (bots) can result in high variance in the estimates of CTR. To improve the estimation accuracy of user experience metrics like CTR, we argue that it is important to identify typical and atypical user sessions in clickstreams. Our approach to identify these sessions is based on detecting outliers using Mahalanobis distance in the user session space. Our user session model incorporates several key clickstream characteristics including a novel conformance score obtained by Markov Chain analysis. Editorial results show that our approach of identifying typical and atypical sessions has a precision of about 89%. Filtering out these atypical sessions reduces the uncertainty (95% confidence interval) of the mean CTR by about 40%. These results demonstrate that our approach of identifying typical and atypical user sessions is extremely valuable for cleaning "noisy" user session data for increased accuracy in evaluating user experience.
Decoding the androgen receptor splice variants. (2013)

In the past five years, multiple structurally and functionally distinct androgen receptor (AR) splice variants have been decoded and characterized. The mature transcripts for the majority of the fully decoded AR splice variants contain a transcribed "intronic" sequence, capable of encoding a short variant-specific peptide to replace the AR ligand-binding domain (LBD). Functionally, AR splice variants represent a diverse group of molecules often demonstrating cell context-specific genomic functions that may or may not be coupled with the functions of the canonical full-length AR (AR-FL). However, the full spectrum of their functional diversity and the underlying mechanistic basis remains very poorly characterized. In clinical specimens derived from men treated with a variety of hormone therapy regimens, AR splice variants are almost always expressed at detectable, yet lower levels when compared to that of AR-FL. In spite of the collective <i>in vitro</i> data supporting the putative role of AR splice variants in therapeutic resistance to hormone therapies, the extent to which AR splice variants mediate resistance to each individual regimen is not known and awaits thorough investigations in a clinically relevant setting using specimens from men undergoing treatments. Among the AR splice variants, AR-V7 is more abundantly and frequently expressed in castration-resistant prostate cancer (CRPC) and remains the most important variant identified so far. The relative importance of different AR molecules, including AR-FL, should be functionally dissected in the setting of castration-resistant prostate cancer, particularly in tumors resistant to more potent inhibitors of AR-FL recently approved by the FDA. In this review, we will focus on the discovery and characterization of AR splice variants, their putative functions and roles in mediating constitutively active AR signaling, and key areas of investigation that are necessary to establish their clinical relevance.
Simplified check node processing in nonbinary LDPC decoders (2010)

This paper deals with low-complexity algorithms for the check node processing in nonbinary LDPC decoders. After a review of the state-of-the-art, we focus on an original solution to significantly reduce the order of complexity of the Extended Min-Sum decoder at the elementary check node level. The main originality of the so-called Bubble Check algorithm is the two-dimensional strategy for the check node processing, which leads to a reduction of the number of comparisons. The simulation results obtained for the Bubble Check show that this complexity reduction does not introduce any performance loss and that it is even possible to further reduce the number of comparisons. This motivated the search of a simplified architecture and led to the L-Bubble Check, which is the main contribution of the paper. The implementation of a forward/backward check node as a systolic architecture of L-Bubble elementary checks is also described. Finally, some FPGA synthesis results of a whole GF(64)-LDPC decoder implementation are presented.
GPS-based remote sensing of the geospace environment: horizontal and vertical structure of the ionosphere and plasmasphere (2004)

Transmissions of the Global Positioning System (GPS) satellites can be used to measure the total electron content (TEC) between a receiver and several GPS satellites in view. This simple observable is yielding a wealth of new scientific information about ionosphere and plasmasphere dynamics. Data available from thousands of ground-based GPS receivers are used to image the large-scale and mesoscale ionospheric response to geospace forcings at high-precision covering all local times and latitudes. Complementary measurements from space-borne GPS receivers in low-Earth orbit provide information on both vertical and horizontal structure of the ionosphere/plasmasphere system. New flight hardware designs are being developed that permit simultaneous measurement of integrated electron content along new raypath orientations, including zenith, cross-track and nadir antenna orientations (the latter via bistatic reflection of the GPS signal off ocean surfaces). We will discuss a new data assimilation model of ionosphere, the Global Assimilative Ionosphere Model (GAIM), capable of integrating measurements from GPS and other sensors with a physics-based ionospheric model, to provide detailed global nowcasts of ionospheric structure, useful for science and applications. Finally, we discuss efforts underway to combine GPS space-based observations of plasmaspheric TEC, with ground-based magnetometer measurements, and satellite-based images from NASA's IMAGE satellite, to produce new dynamic models of the plasmasphere.
Novel Insulinoma Cell Lines Produced by Iterative Engineering of GLUT2, Glucokinase, and Human Insulin Expression (1997)

Cellular engineering studies in our group are directed at creating insulin-secreting cell lines that simulate the performance of the normal islet beta-cell. The strategy described in this article involves the stepwise stable introduction of genes relevant to beta-cell performance into the RIN 1046-38 insulinoma cell line, a process that we term "iterative engineering." RIN cells stably engineered to contain multiple copies of the human insulin gene exhibit a large increase in insulin content, such that they approach the content of human islets assayed in parallel. Analysis by high-performance liquid chromatography demonstrates that these engineered cell lines process human proinsulin to mature insulin with high efficiency. Cell lines that are further engineered to express the GLUT2 and glucokinase genes demonstrate stable expression of the three transgenes for the full lifetime of the lines produced to date (6 months to 1 year in continuous culture). Transplantation of the engineered cell lines into nude rats reveals that stably integrated genes are expressed at constant levels in the in vivo environment over the full duration of experiments performed (48 days). Several endogenous genes expressed in normal beta-cells, including rat insulin, amylin, sulfonylurea receptor, and glucokinase, are stably expressed in the insulinoma lines during these in vivo studies. Endogenous GLUT2 expression, in contrast, is rapidly extinguished during in vivo passage. The loss of GLUT2 is overcome in engineered cell ines in which transporter expression is provided by a stably transfected transgene. These results suggest that a potential advantage of the iterative engineering approach may be to preserve stability of function and phenotype, particularly in the in vivo setting.
Short Linear Cationic Antimicrobial Peptides: Screening, Optimizing, and Prediction (2008)

The problem of pathogenic antibiotic-resistant bacteria such as Staphylococcus aureus and Pseudomonas aeruginosa is worsening, demonstrating the urgent need for new therapeutics that are effective against multidrug-resistant bacteria. One potential class of substances is cationic antimicrobial peptides. More than 1000 natural occurring peptides have been described so far. These peptides are short (less than 50 amino acids long), cationic, amphiphilic, demonstrate different three-dimensional structures, and appear to have different modes of action. A new screening assay was developed to characterize and optimize short antimicrobial peptides. This assay is based on peptides synthesized on cellulose, combined with a bacterium, where a luminescence gene cassette was introduced. With help of this method tens of thousands of peptides can be screened per year. Information gained by this high-throughput screening can be used in quantitative structure-activity relationships (QSAR) analysis. QSAR analysis attempts to correlate chemical structure to measurement of biological activity using statistical methods. QSAR modeling of antimicrobial peptides to date has been based on predicting differences between peptides that are highly similar. The studies have largely addressed differences in lactoferricin and protegrin derivatives or similar de novo peptides. The mathematical models used to relate the QSAR descriptors to biological activity have been linear models such as principle component analysis or multivariate linear regression. However, with the development of high-throughput peptide synthesis and an antibacterial activity assay, the numbers of peptides and sequence diversity able to be studied have increased dramatically. Also, "inductive" QSAR descriptors have been recently developed to accurately distinguish active from inactive drug-like activity in small compounds. "Inductive" QSAR in combination with more complex mathematical modeling algorithms such as artificial neural networks (ANNs) may yield powerful new methods for in silico identification of novel antimicrobial peptides.
TRO: An On-Chip Ring Oscillator-Based GHz Transient IR-Drop Monitor (2016)

With silicon technology further scaling, the switching activity is getting more intense in modern designs. The large switching activities together with GHz operation frequency can greatly affect the power integrity by generating IR-drop noises. Excessive IR-drop can cause functional failures such as timing failure, abnormal reset and SRAM flipping. Hence, IR-drop needs to be monitored in-field. However, directly measuring transient IR-drop waveform usually involves high design or equipment cost. This paper presents a low-cost on-chip GHz ring oscillator-based transient IR-drop monitor (TRO). TRO is composed of all-digital elements, and can be easily integrated into existing IC design flow with negligible overhead. Different from traditional transient IR-drop monitors, TRO measures IR-drop waveform width and average in-field, while recovers IR-drop peak, and reconstructs the transient noise waveform during data analysis or customer return, which eliminates the need for custom circuits or high frequency sampling clock. Simulation results show that TRO is sensitive to IR-drop with peak and width larger than 100 mV and 1.0 ns, which is suitable for GHz IC monitoring. The IR-drop noise width detection resolution can reach 0.125 ns and higher under the help of the proposed edge detector, with noise peak and width measurement error rate less than 6.8% and 9.0%, for 97% of the Monte Carlo samples considering process variations. According to the results and analyses, TRO is also able to trigger quick adaptation within one clock cycle.
Vascular Leakage in Severe Dengue Virus Infections: A Potential Role for the Nonstructural Viral Protein NS1 and Complement (2006)

Complement activation mediated by NS1 leads to local and systemic generation of anaphylatoxins and SC5b-9, which may contribute to the pathogenesis of the vascular leakage that occurs in patients with DHF/DSS.