gebhart/patrepeval huggingface dataset:
Ulcerative colitis disease activity following treatment of associated primary sclerosing cholangitis with cyclosporin. (1993)

Thirty five adult patients with precirrhotic primary sclerosing cholangitis were randomly allocated to treatment for at least one year with low dose (4.1 mg/kg/day) cyclosporin or placebo in a double blind trial. Thirty patients had coexisting ulcerative colitis, including three who had previously undergone colectomy and one who discontinued treatment after three months. Of the remaining 26 patients, 16 received cyclosporin and 10 received placebo. Endoscopy was performed at entry to confirm the diagnosis of inflammatory bowel disease. The ulcerative colitis disease activity was prospectively classified annually as remission/mild, moderate, or severe using the Truelove and Witt's criteria. Before treatment there were no differences between the cyclosporin and placebo groups in the number of patients with remission/mild colitis, 14/16 (88%) v 9/10 (90%), and moderate colitis, 2/16 (12%) v 1/10 (10%). During treatment, a remission/mild disease course was present in 15/16 (94%) v 6/10 (60%), p = 0.05 and a moderate disease course in 1/16 (6%) v 4/10 (40%), p = 0.05. It is concluded that patients treated with cyclosporin for primary sclerosing cholangitis who have coexisting ulcerative colitis have a more benign course of colitis resulting both from improvement of moderately active colitis and from fewer flares of remission/mildly active colitis. These findings suggest that cyclosporin may be of benefit to the colon in patients with ulcerative colitis who are being treated with cyclosporin for primary sclerosing cholangitis.
oXirisNet Registry: A Prospective, National Registry on the oXiris Membrane (2019)

Worldwide, the widespread use of extracorporeal blood purification therapies (EBPTs) is progressively increasing in everyday clinical practice, particularly in critical care settings. The efficacy of EBPTs on removal of inflammatory mediators is already well established in the literature. Nonetheless, clinical research is particularly cumbersome in this setting, and many clinical trials aiming at exploring the effect of EBPTs on outcomes have failed in demonstrating consistent results regarding 28-day- or hospital-mortality rates. In recent years, data emerging from large registries have been increasingly used to provide real-world evidence on the effectiveness, quality, and safety of EBPTs. The philosophy behind this Italian Registry is a renewal of the concept of "clinical research" in the field of EBPTs applied to critically ill, septic patients with or without acute kidney injury. The platform used for the registry - specifically designed for research purposes and fed by clinical data prospectively observed - promotes good practice with a positive and active interaction with the physician/researcher. This interaction has favorable real-time effects for the specific patient, providing "bed-side clinical feedbacks," similarly to the decision support system. Examples of these issues are bundles reminders, suggestions for drug adjustment according to the extracorporeal clearance, clinical calculator for body mass index, or mechanical ventilation setting. The platform-physician interaction has additional useful effects on the single utilizing center, providing "mid-term, center-specific clinical feedbacks." These generally consist of clusters of data taken over a certain period, for example, regarding patients' outcome, microbiological data, or use of disposable for EBPTs.
Structure and Function of NzeB, a Versatile C–C and C–N Bond-Forming Diketopiperazine Dimerase (2020)

The dimeric diketopiperazine (DKPs) alkaloids are a diverse family of natural products (NPs) whose unique structural architectures and biological activities have inspired the development of new synthetic methodologies to access these molecules. However, catalyst-controlled methods that enable the selective formation of constitutional and stereoisomeric dimers from a single monomer are lacking. To resolve this long-standing synthetic challenge, we sought to characterize the biosynthetic enzymes that assemble these NPs for application in biocatalytic syntheses. Genome mining enabled identification of the cytochrome P450, NzeB (<i>Streptomyces</i> sp. NRRL F-5053), which catalyzes both intermolecular carbon-carbon (C-C) and carbon-nitrogen (C-N) bond formation. To identify the molecular basis for the flexible site-selectivity, stereoselectivity, and chemoselectivity of NzeB, we obtained high-resolution crystal structures (1.5 Å) of the protein in complex with native and non-native substrates. This, to our knowledge, represents the first crystal structure of an oxidase catalyzing direct, intermolecular C-H amination. Site-directed mutagenesis was utilized to assess the role individual active-site residues play in guiding selective DKP dimerization. Finally, computational approaches were employed to evaluate plausible mechanisms regarding NzeB function and its ability to catalyze both C-C and C-N bond formation. These results provide a structural and computational rationale for the catalytic versatility of NzeB, as well as new insights into variables that control selectivity of CYP450 diketopiperazine dimerases.
Cold-Knife Endoureterotomy for Nonmalignant Ureterointestinal Anastomotic Strictures (2004)

No AccessJournal of UrologyUrological Survey: ABSTRACTS: UROLITHIASIS, ENDOUROLOGY AND LAPAROSCOPY1 Aug 2004Cold-Knife Endoureterotomy for Nonmalignant Ureterointestinal Anastomotic Strictures Ralph V. ClaymanM.D. Ralph V. ClaymanRalph V. Clayman More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(05)61779-XAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Cold-Knife Endoureterotomy for Nonmalignant Ureterointestinal Anastomotic Strictures." The Journal of Urology, 172(2), pp. 799–800 References 1 : Long-term results of endoureterotomy for benign ureteral and ureteroenteric strictures. J Urol1997; 158: 759. Google Scholar © 2004 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 172Issue 2August 2004Page: 799-800 Advertisement Copyright & Permissions© 2004 by American Urological Association, Inc.MetricsAuthor Information Ralph V. Clayman More articles by this author Expand All Advertisement Loading ...
Observation of Two Photon Absorption Prior to Laser-Induced Damage in ZrO2 (1988)

We observed substantial dispersion in the breakdown electric field for yttria stabilized cubic zirconia (Zr02). The measured breakdown field at 1064 run is a factor of 5 larger than that at 532 nm for 18 nsec (FWHM) pulses. For 532 run pulses, we measured a significant decrease in transmission prior to the observation of catastrophic damage (i.e., damage accompanied by a spark and fracture of the sample). The observed nonlinear transmission is attributed to absorption by color centers generated by two-photon absorption (2PA). Presence of the color centers were directly monitored by transmission measurements. A permanent change in transmission was measured by irradiating the samples at high intensities (300 MW/cm2). These induced defects are long lived (on the order of hours) but can be bleached by repeated irradiation with relatively low intensities (20 MW/cm2). In a separate experiment, using picosecond pulses at 532 nm, the 2PA coefficient was determined to be 0.015 cm/GW.
Continuous-Time Delta-Sigma Controller for DC-DC Converter (2015)

This paper describes applications of a Delta-Sigma (ΔΣ) modulator to control a DC-DC converter. We propose to use a continuous-time (CT) feed-forward (FF) ΔΣ controller in a DC-DC converter and show that its transient response is faster than discrete-time (DT) and/or feedback-type (FB) ΔΣ controllers. We have also performed experiments of a DC-DC converter with a first-order continuous-time feedback ΔΣ controller and show its results.
Key establishment in large dynamic groups using one-way function trees (2003)

We present, implement, and analyze a new scalable centralized algorithm, called OFT, for establishing shared cryptographic keys in large, dynamically changing groups. Our algorithm is based on a novel application of one-way function trees. In comparison with the top-down logical key hierarchy (LKH) method of Wallner et al., our bottom-up algorithm approximately halves the number of bits that need to be broadcast to members in order to rekey after a member is added or evicted. The number of keys stored by group members, the number of keys broadcast to the group when new members are added or evicted, and the computational efforts of group members, are logarithmic in the number of group members. Among the hierarchical methods, OFT is the first to achieve an approximate halving in broadcast length, an idea on which subsequent algorithms have built. Our algorithm provides complete forward and backward security: Newly admitted group members cannot read previous messages, and evicted members cannot read future messages, even with collusion by arbitrarily many evicted members. In addition, and unlike LKH, our algorithm has the option of being member contributory in that members can be allowed to contribute entropy to the group key. Running on a Pentium II, our prototype has handled groups with up to 10 million members. This algorithm offers a new scalable method for establishing group session keys for secure large-group applications such as broadcast encryption, electronic conferences, multicast sessions, and military command and control.
Combat casualty care research for the multidomain battlefield (2017)

Rasmussen, Todd E. MD; Baer, David G. PhD; Remick, Kyle N. MD; Ludwig, George V. PhD Author Information
Genomic analysis of theTapasin gene, located close to theTAP loci in the MHC (1998)

The Tapasin molecule is a member of the immunoglobulin (Ig) superfamily required for the association of TAP transporters and MHC class I heterodimers in the endoplasmic reticulum. In this study, the Tapasin gene was precisely mapped in relation to the MHC. The gene was centromeric of the HLA-DP locus between the HSET and HKE1.5 genes and within 500 kbp of the TAP1 and TAP2 genes. A homologous mouse EST was mapped to a syntenic position on chromosome 17, centromeric of the H-2 K locus. Similarly, the rat Tapasin gene was shown to be in an equivalent location with respect to the RT1.A locus. The localization of Tapasin, TAP, LMP and class I genes within such a short distance of each other on the chromosome implies some regulatory or functional significance. We determined the Tapasin gene sequence for comparison of its structure to that of other Ig superfamily members, such as MHC class I genes. The IgC domain was encoded by a separate exon. However, the positions of the other introns were not characteristic of other Ig superfamily genes, indicating that Tapasin has a distinct phylogeny.
Fiber array phase cohering: holographic vs numerical (2006)

Coherent optical systems can be fed by phase cohered fiber arrays that maintain constant phase across the array. We present and compare results for arrays cohered by holography, redundant spacing calibration, and optical self-calibration.
A Comparison of Contextual Bandit Approaches to Human-in-the-Loop Robot Task Completion with Infrequent Feedback (2019)

Artificially intelligent assistive agents are playing an increased role in our work and homes. In contrast with currently predominant conversational agents, whose intelligence derives from dialogue trees and external modules, a fully autonomous domestic or workplace robot must carry out more complex reasoning. Such a robot must make good decisions as soon as possible, learn from experience, respond to feedback, and rely on feedback only as much as necessary. In this research, we narrow the focus of a hypothetical robot assistant to a room-tidying task in a simulated domestic environment. Given an item, the robot chooses where to put it among many destinations, then optionally receives feedback from a human operator. We frame the problem as a contextual bandit, a reinforcement learning approach frequently used in Web recommendation systems. We evaluate epsilon-greedy and LinUCB action selection methods under a variety of infrequent feedback scenarios, with several methods for managing the lack of feedback. Our empirical results show that, while early-episode performance and overall accuracy of epsilon-greedy action selection can be improved through learning from no-response feedback and careful management of remembered training episodes, a baseline LinUCB approach outperforms epsilon-greedy action selection in early-episode performance, overall accuracy, and simplicity.
En‐face optical coherence tomography for the detection of cancer in prostatectomy specimens: Quantitative analysis in 20 patients (2020)

The increase histopathological evaluation of prostatectomy specimens rises the workload on pathologists. Automated histopathology systems, preferably directly on unstained specimens, would accelerate the pathology workflow. In this study, we investigate the potential of quantitative analysis of optical coherence tomography (OCT) to separate benign from malignant prostate tissue automatically. Twenty fixated prostates were cut, from which 54 slices were scanned by OCT. Quantitative OCT metrics (attenuation coefficient, residue, goodness-of-fit) were compared for different tissue types, annotated on the histology slides. To avoid misclassification, the poor-quality slides, and edges of annotations were excluded. Accurate registration of OCT data with histology was achieved in 31 slices. After removing outliers, 56% of the OCT data was compared with histopathology. The quantitative data could not separate malignant from benign tissue. Logistic regression resulted in malignant detection with a sensitivity of 0.80 and a specificity of 0.34. Quantitative OCT analysis should be improved before clinical use.
Quantification of myocardial late gadolinium enhancement using synthetic inversion recovery imaging (2015)

Background Inversion recovery (IR) late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) is generally used for post-contrast infarct detection in the myocardium. Novel technological advancements allow for the generation of synthetic IR images based on the pixel-bypixel T1 values. Theoretically, synthetic IR images can be retrospectively generated at any inversion time (TI). In this study, we aimed to evaluate the diagnostic value of synthetic phase-sensitive IR (PSIR) images for the quantification of myocardial LGE. Methods
Acoustic performance of an installed real-time three-dimensional audio system. (2010)

The Exterior Effects Room (EER), located at the NASA Langley Research Center, is a facility built for psychoacoustic studies of aircraft community noise. Recently, the EER was significantly upgraded to allow for simulation of aircraft flyovers in a 3-D audio and visual environment. The upgrade included installation of 27 satellite and 4 subwoofer loudspeakers that are driven by a real-time audio server. The audio server employs an implementation of the vector base amplitude panning method to position virtual sources at arbitrary azimuth and elevation angles in the EER. Real-time application of filters, time delays, and gains are required to compensate for installation effects, including those associated with the irregular room geometry, colorization due to varying loudspeaker installations, and crossover filtering. The authors previously showed [J. Acoust. Soc. Am., 127, 1969 (2010)] that color compensation and crossover filtering could be achieved for satellite and subwoofer loudspeakers. However, the resulting FIR filters were too long (32 768 taps) to implement in real-time. The focus of this work is on the development of reduced-length surrogate IIR filters and on the measurement of the acoustic performance of the installed real-time system.
Obesity-associated changes in molecular biology of primary breast cancer (2023)

Obesity is associated with an increased risk of developing breast cancer (BC) and worse prognosis in BC patients, yet its impact on BC biology remains understudied in humans. This study investigates how the biology of untreated primary BC differs according to patients' body mass index (BMI) using data from >2,000 patients. We identify several genomic alterations that are differentially prevalent in overweight or obese patients compared to lean patients. We report evidence supporting an ageing accelerating effect of obesity at the genetic level. We show that BMI-associated differences in bulk transcriptomic profile are subtle, while single cell profiling allows detection of more pronounced changes in different cell compartments. These analyses further reveal an elevated and unresolved inflammation of the BC tumor microenvironment associated with obesity, with distinct characteristics contingent on the estrogen receptor status. Collectively, our analyses imply that obesity is associated with an inflammaging-like phenotype. We conclude that patient adiposity may play a significant role in the heterogeneity of BC and should be considered for BC treatment tailoring.
Cationic Polyelectrolyte for Anionic Cyanines: An Efficient Way To Translate Molecular Properties into Material Properties (2019)

In this work, a new phosphonium-containing cationic polyelectrolyte (<b>PE1</b>) has been rationally designed and developed via a facile click-chemistry type postfunctionalization, which can form complexes with highly polarizable anionic cyanines to significantly reduce the strong and random cyanine-cyanine interactions (i.e., aggregation) in the solid-state. This material design strategy enables an efficient translation of the favorable molecular properties of cyanines into macroscopic material properties. One of such complexes exhibits a very large third-order susceptibility over 10<sup>-10</sup> esu with low nonlinear optical loss suitable for all optical signal processing.
Application to the Analysis of Truncated Transcripts of the Dystrophin Gene in Nonmuscle Cultured Cells from Duchenne and Becker Patients (1991)

We have previously demonstrated that there is a low level of transcription of tissue-specific genes in every cell type. In this study, we have taken advantage of this phenomenon, called illegitimate transcription, to analyze the muscle-type dystrophin mRNA in easily accessible cells such as lymphoid cells, fibroblasts, and peripheral blood cells from Duchenne and Becker muscular dystrophies with known internal gene deletion. The results showed that, in the studied regions surrounding the deletions, processing of truncated transcripts is identical in specific (muscle tissue) and in nonspecific cells (lymphoid cells). In Becker cases with out-of-frame deletions, the already described alternatively spliced species found in muscle samples were also found in nonspecific cells. These results demonstrate that illegitimate transcripts are a bona fide version of tissuespecific mRNA, and that they represent a useful material to investigate the qualitative consequences of gene defects at the mRNA level. (J. Clin. Invest. 1991. 88:1161-1166.) Key
Micron: An Actively Stabilized Handheld Tool for Microsurgery (2011)

We describe the design and performance of a hand-held actively stabilized tool to increase accuracy in micro-surgery or other precision manipulation. It removes involuntary motion such as tremor by actuating the tip to counteract the effect of the undesired handle motion. The key components are a three-degree-of-freedom piezoelectric manipulator that has 400 μm range of motion, 1 N force capability, and bandwidth over 100 Hz, and an optical position measurement subsystem that acquires the tool pose with 4 μm resolution at 2000 samples/s. A control system using these components attenuates hand motion by at least 15 dB (a fivefold reduction). By considering the effect of the frequency response of Micron on the human visual feedback loop, we have developed a filter that reduces unintentional motion, yet preserves intuitive eye-hand coordination. We evaluated the effectiveness of Micron by measuring the accuracy of the human/machine system in three simple manipulation tasks. Handheld testing by three eye surgeons and three non-surgeons showed a reduction in position error of between 32% and 52%, depending on the error metric.
Recombinant Retroviruses Encoding Simian Virus 40 Large T Antigen and Polyomavirus Large and Middle T Antigens (1986)

We used a murine retrovirus shuttle vector system to construct recombinants capable of constitutively expressing the simian virus 40 (SV40) large T antigen and the polyomavirus large and middle T antigens as well as resistance to G418. Subsequently, these recombinants were used to generate cell lines that produced defective helper-free retroviruses carrying each of the viral oncogenes. These recombinant retroviruses were used to analyze the role of the viral genes in transformation of rat F111 cells. Expression of the polyomavirus middle T antigen alone resulted in cell lines that were highly tumorigenic, whereas expression of the polyomavirus large T resulted in cell lines that were highly tumorigenic, whereas expression of the polyomavirus large T resulted in cell lines that were unaltered by the criteria of morphology, anchorage-independent growth, and tumorigenicity. More surprisingly, SV40 large T-expressing cell lines were not tumorigenic despite the fact that they contained elevated levels of cellular p53 and had a high plating efficiency in soft agar. These results suggest that the SV40 large T antigen is not an acute transforming gene like the polyomavirus middle T antigen but is similar to the establishment genes such as myc and adenovirus EIa.
<title>Challenges and opportunities for migration towards 10GPON</title> (2009)

Different technical challenges for migration from GPON to 10GPON are discussed and also put into context of standardization. The challenges include how to handle an increased upstream capacity through use of burst-mode receivers and DBA algorithms, extension of reach and wavelength planning for future proofing the fiber infrastructure. Finally the roadmap towards 10GPON standardization is discussed.
Zone division model for capacity analysis in multi-hop data acquisition systems with hidden nodes (2013)

Data acquisition systems play an important role in several industries. Because highly scalable ad-hoc networks with multi-hop transmissions can be easily constructed at low cost, such networks are considered suitable for data acquisition systems. However, a lack of centralized control makes it difficult to respond to congestion when system capacity is exceeded. Therefore, the estimation of system capacity is a critical issue for system design. In this paper, we propose a novel zone division model to analyze the capacity of multi-hop data acquisition systems using Carrier Sense Multiple Access with Collision Avoidance (CSMA/CA) protocols. We divide the one-hop area to a gateway (GW) into two zones: (1) an outer zone where an access node (AN) can relay packets from multi-hop ANs; and (2) an inner zone where ANs cannot relay packets. Using this approach, we calculate packet loss for each zone, considering the difference in the communication range of the GW and ANs, as well as the collision with hidden nodes. Simulation results show that our model achieves higher estimation accuracy than conventional methods, indicating that we have successfully modeled phenomena of the real system more accurately.