gebhart/patrepeval huggingface dataset:
Ratiometric Pulse–Chase Amidination Mass Spectrometry as a Probe of Biomolecular Complex Formation (2011)

Selective chemical modification of protein side chains coupled with mass spectrometry is often most informative when used to compare residue-specific reactivities in a number of functional states or macromolecular complexes. Herein, we develop ratiometric pulse-chase amidination mass spectrometry (rPAm-MS) as a site-specific probe of lysine reactivities at equilibrium using the Cu(I)-sensing repressor CsoR from Bacillus subtilis as a model system. CsoR in various allosteric states was reacted with S-methyl thioacetimidate (SMTA) for pulse time, t, and chased with excess of S-methyl thiopropionimidate (SMTP) (Δ = 14 amu), quenched and digested with chymotrypsin or Glu-C protease, and peptides were quantified by high-resolution matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and/or liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). We show that the reactivities of individual lysines from peptides containing up to three Lys residues are readily quantified using this method. New insights into operator DNA binding and the Cu(I)-mediated structural transition in the tetrameric copper sensor CsoR are also obtained.
The Recovery of Cognitive Function After Remifentanil- Nitrous Oxide Anesthesia Is Faster than After an Isoflurane-Nitrous Oxide-Fentanyl Combination in Elderly Patients (2000)

We tested the hypothesis that remifentanil-nitrous oxide (N2O) anesthesia shortens postoperative emergence and recovery compared with an isoflurane-N2O-fentanyl combination in elderly patients undergoing spinal surgery. A total of 60 patients (>65 yr old) were randomly assigned to one of two groups for maintenance of anesthesia. After the induction with 3.6 ± 1.2 mg/kg IV thiopental and endotracheal intubation facilitated with 1.4 ± 0.5 mg/kg succinylcholine, patients were maintained with either 0.5%–1.5% isoflurane, 70% N2O, and up to 7 μg/kg fentanyl (iso/fent group) or 48 ± 11 μg/kg remifentanil and 70% N2O (remi group). A mini-mental status examination was used to assess cognitive ability preoperatively, at 15, 30, and 60 min after arrival at the postanesthesia care unit and again 12–24 h postoperatively. The time from the conclusion of anesthesia to spontaneous respiration was similar in both groups. Times to eye opening (4.8 ± 2.6 vs 2.3 ± 1.1 min), extubation (6.8 ± 3.8 vs 3.2 ± 2.1 min), and verbalization (9.9 ± 6.2 vs 3.9 ± 2.6 min) were significantly shorter for the remi group (P < 0.05). Postoperative mini-mental status examination scores were significantly lower in the iso/fent group at 15 (16.3 ± 5.8 vs 23.7 ± 3.3), 30 (20.2 ± 5.2 vs 26.3 ± 2.7), and 60 min (23.5 ± 4.4 vs 27.5 ± 2.0) (P < 0.001); however, the scores equalized after 12 h. Requirements for postoperative analgesics were similar in the two groups. More patients in the remi group were treated with antiemetics (21 vs 7, P = 0.06). Use of remifentanil-N2O for maintenance did not shorten the overall length of stay in the postanesthesia care unit; a stay is often related to multiple administrative issues, rather than cognitive recovery. Implications Maintenance of anesthesia with remifentanil-nitrous oxide (N2O), compared with isoflurane-N2O-fentanyl, can safely shorten postoperative recovery of cognitive function in a geriatric population. Earlier recovery may facilitate postoperative neurological assessment. Use of remifentanil-N2O for maintenance did not shorten the overall length of stay in the postanesthesia care unit, a stay often related to multiple administrative issues, rather than cognitive recovery.
CLIPasso (2022)

Abstraction is at the heart of sketching due to the simple and minimal nature of line drawings. Abstraction entails identifying the essential visual properties of an object or scene, which requires semantic understanding and prior knowledge of high-level concepts. Abstract depictions are therefore challenging for artists, and even more so for machines. We present CLIPasso, an object sketching method that can achieve different levels of abstraction, guided by geometric and semantic simplifications. While sketch generation methods often rely on explicit sketch datasets for training, we utilize the remarkable ability of CLIP (Contrastive-Language-Image-Pretraining) to distill semantic concepts from sketches and images alike. We define a sketch as a set of Bézier curves and use a differentiable rasterizer to optimize the parameters of the curves directly with respect to a CLIP-based perceptual loss. The abstraction degree is controlled by varying the number of strokes. The generated sketches demonstrate multiple levels of abstraction while maintaining recognizability, underlying structure, and essential visual components of the subject drawn.
In situ High‐Field Dynamic Nuclear Polarization—Direct and Indirect Polarization of 13C nuclei (2010)

In situ High-Field Dynamic Nuclear Polarization: Direct and indirect polarization of 13C nuclei by DNP is investigated (see graphic). The field-dependent enhancement profile for both processes are investigated and the bulk polarization build-up time constants τBC and τBH for direct and indirect 13C polarization are compared.
The VP7 Outer Capsid Protein of Rotavirus Induces Polyclonal B-Cell Activation (2004)

The early response to a homologous rotavirus infection in mice includes a T-cell-independent increase in the number of activated B lymphocytes in the Peyer's patches. The mechanism of this activation has not been previously determined. Since rotavirus has a repetitively arranged triple-layered capsid and repetitively arranged antigens can induce activation of B cells, one or more of the capsid proteins could be responsible for the initial activation of B cells during infection. To address this question, we assessed the ability of rotavirus and virus-like particles to induce B-cell activation in vivo and in vitro. Using infectious rotavirus, inactivated rotavirus, noninfectious but replication-competent virus, and virus-like particles, we determined that neither infectivity nor RNA was necessary for B-cell activation but the presence of the rotavirus outer capsid protein, VP7, was sufficient for murine B-cell activation. Preincubation of the virus with neutralizing VP7 antibodies inhibited B-cell activation. Polymyxin B treatment and boiling of the virus preparation were performed, which ruled out possible lipopolysaccharide contamination as the source of activation and confirmed that the structural conformation of VP7 is important for B-cell activation. These findings indicate that the structure and conformation of the outer capsid protein, VP7, initiate intestinal B-cell activation during rotavirus infection.
Polymyxin derivatives: a patent evaluation (WO2012168820) (2013)

The patent application WO201268820 claims a new class of polymyxin derivatives with potent antibacterial activity, especially toward Gram-negative pathogens. Compared to parent polymyxin B (PMB), the new derivatives have more potent antibacterial activity, as well as reduced cytotoxicity against human renal cells.
Modeling the baseband output envelope of a Microwave detector (2009)

The current state-of-the-art for the calibration of wave spectra containing spectral lines that lie on a harmonic grid (f0, 2f0...) relies on the well-established step recovery diode method [1]. The challenge in narrow band modulated measurements
The use of grayscale for improved raster display of vectors and characters (1978)

Decreasing memory costs will soon allow grayscale displays in low-cost raster graphic terminals. Subtle shadings can be used to provide improvements in line quality and character flexibility which could allow raster displays to compete on better terms with the more expensive calligraphic displays. Algorithms for achieving smooth vectors and rotatable dot matrix characters are outlined and scan conversion is discussed. A discussion of the relation between image quality and number and distribution of gray levels follows, with concluding remarks on costs and other practical matters.
Inotersen Treatment for Patients with Hereditary Transthyretin Amyloidosis (2018)

BACKGROUND: Hereditary transthyretin amyloidosis is caused by pathogenic single-nucleotide variants in the gene encoding transthyretin ( TTR) that induce transthyretin misfolding and systemic deposition of amyloid. Progressive amyloid accumulation leads to multiorgan dysfunction and death. Inotersen, a 2'- O-methoxyethyl-modified antisense oligonucleotide, inhibits hepatic production of transthyretin. METHODS: We conducted an international, randomized, double-blind, placebo-controlled, 15-month, phase 3 trial of inotersen in adults with stage 1 (patient is ambulatory) or stage 2 (patient is ambulatory with assistance) hereditary transthyretin amyloidosis with polyneuropathy. Patients were randomly assigned, in a 2:1 ratio, to receive weekly subcutaneous injections of inotersen (300 mg) or placebo. The primary end points were the change in the modified Neuropathy Impairment Score+7 (mNIS+7; range, -22.3 to 346.3, with higher scores indicating poorer function; minimal clinically meaningful change, 2 points) and the change in the score on the patient-reported Norfolk Quality of Life-Diabetic Neuropathy (QOL-DN) questionnaire (range, -4 to 136, with higher scores indicating poorer quality of life). A decrease in scores indicated improvement. RESULTS: A total of 172 patients (112 in the inotersen group and 60 in the placebo group) received at least one dose of a trial regimen, and 139 (81%) completed the intervention period. Both primary efficacy assessments favored inotersen: the difference in the least-squares mean change from baseline to week 66 between the two groups (inotersen minus placebo) was -19.7 points (95% confidence interval [CI], -26.4 to -13.0; P<0.001) for the mNIS+7 and -11.7 points (95% CI, -18.3 to -5.1; P<0.001) for the Norfolk QOL-DN score. These improvements were independent of disease stage, mutation type, or the presence of cardiomyopathy. There were five deaths in the inotersen group and none in the placebo group. The most frequent serious adverse events in the inotersen group were glomerulonephritis (in 3 patients [3%]) and thrombocytopenia (in 3 patients [3%]), with one death associated with one of the cases of grade 4 thrombocytopenia. Thereafter, all patients received enhanced monitoring. CONCLUSIONS: Inotersen improved the course of neurologic disease and quality of life in patients with hereditary transthyretin amyloidosis. Thrombocytopenia and glomerulonephritis were managed with enhanced monitoring. (Funded by Ionis Pharmaceuticals; NEURO-TTR ClinicalTrials.gov number, NCT01737398 .).
Analysis of the impact of release area on the quality factor of contour-mode resonators by laser Doppler vibrometry (2015)

Energy dissipation through the anchors of an aluminum nitride (AlN) MEMS contour-mode resonator (CMR) plays an important role in setting the device quality factor at frequencies under 500MHz [1]. The acoustic energy leaving the resonator is effected, not only by the anchor, but also the portion of the surrounding device layer that has been released from the substrate during fabrication. Typical device simulations used for design do not take into account the motion of this additional area. Using laser Doppler vibrometery and COMSOL simulations we show a variation in device Q by 28% as a result of the motion of this released region.
Projection optics for EUVL micro-field exposure tools with 0.5 NA (2014)

In last year’s report, we discussed the design and requirements of the optical projection module (Projection Optics Box [POB]) for the 0.5-NA Micro-field Exposure Tool (MET5) and the resulting challenges. Over the course of this past year, we have completed and fully qualified the metrology of individual mirrors. All surface figure errors have been measured over seven orders of magnitude with spatial periods ranging from the full clear aperture down to 10 nm. The reproducibility of the full aperture tests measures 16 pm RMS for the M1 test and 17 pm for the M2 test with a target of 30 pm for both tests. Furthermore, we achieved excellent results on scatter and flare: For scatter, both mirrors perform about a factor of two below specification. For flare, the larger M2 mirror performs well within and the smaller M1 mirror about a factor of two below specification. In addition, we have developed processes for correcting surface figure errors for both mirrors and have successfully demonstrated high-reflectivity coatings on pathfinder mirrors. Further, we have achieved significant goals with respect to the design, assembly, metrology and alignment of the projection module. This paper reviews this progress and describes the next step in the ambitious MET5 POB development program.
XML signature element wrapping attacks and countermeasures (2005)

Naive use of XML Signature may result in signed documents remaining vulnerable to undetected modification by an adversary. In the typical usage of XML Signature to protect SOAP messages, an adversary may be capable of modifying valid messages in order to gain unauthorized access to protected resources.This paper describes the general vulnerability and several related exploits, and proposes appropriate countermeasures. While the attacks described herein may se obvious to security experts once they are explained, effective countermeasures require careful security policy specification and correct implentation by signed message providers and consumers. Since these implenters are not always security experts, this paper provides the guidance necessary to prevent these attacks.
Alpha-Driven Fast Magnetosonic Wave Heating in Tokamak Plasmas (1985)

An alpha-driven fast magnetosonic wave instability is investigated in tokamak plasmas for propagation transverse to the external magnetic field at frequencies several times the alpha gyrorate. A two-dimensional differential quasi-linear diffusion equation is derived in cylindrical υ⊥-υ∥ geometry. The quasi-linear diffusion coefficients in the small parameter k∥/k⊥ are expanded and the problem is reduced to one dimension by integrating out the υ∥ dependence. Reactor relevant information is obtained using data from the one-dimensional formulation in a 1½-dimensional tokamak transport code. Contour plots of the alpha threshold fraction are used to identify the instability regions in the ne-Ti plane. Alpha/background electron fractions as low as 10−6 to 10−4 may trigger the instability. For a typical reactor-size tokamak, an enhancement of the fraction of the alpha energy transferred to ions by as much as 1.5 can occur for Ti = Te at 7 keV. Still, due to the rapid equilibration of electron and ion temperatures, a < 1 to 2% increase in fusion power occurs overall.
Ultrareliable and Low-Latency Communication Techniques for Tactile Internet Services (2018)

This paper presents novel ultrareliable and low-latency communication (URLLC) techniques for URLLC services, such as Tactile Internet services. Among typical use cases of URLLC services are teleoperation, immersive virtual reality, cooperative automated driving, and so on. In such URLLC services, new kinds of traffic such as haptic information including kinesthetic information and tactile information need to be delivered in addition to high-quality video and audio traffic in traditional multimedia services. Furthermore, such a variety of traffic has various characteristics in terms of packet sizes and data rates with a variety of requirements of latency and reliability. Furthermore, some traffic may occur in a sporadic manner but requires reliable delivery of packets of medium to large sizes within a low latency, which is not supported by current state-of-the-art wireless communication systems and is very challenging for future wireless communication systems. Thus, to meet such a variety of tight traffic requirements in a wireless communication system, novel technologies from the physical layer to the network layer need to be devised. In this paper, some novel physical layer technologies such as waveform multiplexing, multiple-access scheme, channel code design, synchronization, and full-duplex transmission for spectrally efficient URLLC are introduced. In addition, a novel performance evaluation approach, which combines a ray-tracing tool and system-level simulation, is suggested for evaluating the performance of the proposed schemes. Simulation results show the feasibility of the proposed schemes providing realistic URLLC services in realistic geographical environments, which encourages further efforts to substantiate the proposed work.
Epstein–barr virus-associated primary b-cell lymphoproliferative disorder of the cerebellum in an immune competent man (1992)

This case demonstrated the development of a primary cerebellar B-cell lymphoproliferative disorder, histologically identical to lymphomatoid granulomatosis, that transformed into a lymphoma. The original tumor and the subsequent lymphoma contained, on average, several copies of EBV-related DNA per cell. Despite an extensive survey of the patient, no immune deficit was detected. Interpretation of the literature with the results of this case suggest that this instance of primary cerebellar LG arose as a consequence of an unusual EBV-associated B-cell lymphoproliferation. It is suggested that EBV may be a significant factor in the initiation of the abnormal proliferations of T-cells or B-cells reported in this disorder.
Full-Wave Formalism for Soliton Propagation in Nonlinear Photonic Crystals (2020)

A full-wave theoretical formalism for the propagation of temporal solitons in 2D Photonic Crystal (PhC) waveguides based on a multi-harmonic treatment (full-wave modal analysis) of the nonlinear setup is presented.
ChemInform Abstract: AMINO ACIDS AND PEPTIDES. CXCI. SOLID PHASE SYNTHESIS AND BIOLOGICAL ACTIVITIES OF OXYTOCIN CARBA ANALOGS CONTAINING THREONINE IN POSITION 4 (1985)

Abstract Die bereits zuvor in Lösung synthetisierten Carba‐oxytocine (Ia) und (Ib) sowie deren [4‐Threonin]‐Analoge (Ic) und (Id) werden durch bekannte Verfahren der Festphasensynthese hergestellt.
Left Ventricular Diastolic Dysfunction in Patients with So‐Called Lone Atrial Fibrillation (2000)

Lone atrial fibrillation (AF) is defined by the absence of identifiable causes of AF, but its hemodynamics have not been investigated. Twenty-eight patients with lone AF were compared with 14 control patients referred for Wolff-Parkinson-White ablation. Transthoracic and transesophageal echocardiography were performed to rule out structural heart disease, followed by transseptally performed complete hemodynamic evaluation of the left heart systolic and diastolic function. There was no evidence of diastolic dysfunction according to echocardiographic criteria in AF and control patients. There was no difference in echocardiographic measurements, except for a significantly higher inferosuperior left atrial dimension seen in the four-chamber apical view in AF patients (51+/-10 vs 40+/-6 mm, P = 0.03). Hemodynamic evaluation showed that end-diastolic left ventricular pressure and the nadir of the left atrial Y descent were significantly higher in lone AF patients versus controls: 13+/-5 versus 8+/-3 mmHg (P = 0.001) and 6.7+/-3 versus 4.6+/-2.7 mmHg (P = 0.05). Our results demonstrated the presence of diastolic left heart dysfunction in patients with so-called lone AF.
Unique Architecture of the Plastid Ribosomal RNA Operon Promoter Recognized by the Multisubunit RNA Polymerase in Tobacco and Other Higher Plants (2003)

Expression of the plastid rRNA operon (rrn) during development is highly regulated at the level of transcription. The plastid rrn operon in most higher plants is transcribed by the plastid-encoded RNA polymerase (PEP), the multisubunit plastid RNA polymerase from PrrnP1, a sigma(70)-type promoter with conserved -10 and -35 core promoter elements. To identify functionally important sequences, the tobacco PrrnP1 was dissected in vivo and in vitro. Based on in vivo deletion analysis, sequences upstream of nucleotide -83 do not significantly contribute to promoter function. The in vitro analyses identified an essential hexameric sequence upstream of the -35 element (GTGGGA; the rRNA operon upstream activator [RUA]) that is conserved in monocot and dicot species and suggested that the -10 element plays only a limited role in PrrnP1 recognition. Mutations in the initial transcribed sequence (+9 to +14) enhanced transcription, the characteristic of strong promoters in prokaryotes. We propose that sigma interaction with the -10 element in PrrnP1 is replaced in part by direct PEP-RUA (protein-DNA) interaction or by protein-protein interaction between the PEP and an RUA binding transcription factor.
Development and comparative evaluation of two antigen detection tests for Visceral Leishmaniasis (2015)

The ELISAs provide a non-invasive method to detect parasite antigens during acute infection and monitor its clearance upon cure, filling an unmet need in VL management. Further refinement of the tests with more samples from endemic regions will define their utility in monitoring treatment.
Amyloid imaging with [18F]florbetapir in geriatric depression: early‐onset versus late‐onset (2014)

Our results showed that the rate of Aβ positivity was higher in late-onset GD and that onset-age was associated with SUVR, suggesting that the later the onset of GD, the more Aβ pathology affected its onset.
Classifying DME vs normal SD-OCT volumes: A review (2016)

This article reviews the current state of automatic classification methodologies to identify Diabetic Macular Edema (DME) versus normal subjects based on Spectral Domain OCT (SD-OCT) data. Addressing this classification problem has valuable interest since early detection and treatment of DME play a major role to prevent eye adverse effects such as blindness. The main contribution of this article is to cover the lack of a public dataset and benchmark suited for classifying DME and normal SD-OCT volumes, providing our own implementation of the most relevant methodologies in the literature. Subsequently, 6 different methods were implemented and evaluated using this common benchmark and dataset to produce reliable comparison.
Experimental aspects of T cell vaccination. (1993)

In the last 10 years, our laboratory has investigated the role of T cells in the induction and therapy of experimental autoimmune diseases. In several animal model T cell lines and clones that were expanded in vitro by repeated culture with the autoantigen were found to be pathogenic. Inoculation of pathogenic T cells after attenuation resulted in protection of the animals against a future attempt to induce the disease: this form of therapy was termed T cell vaccination (TCV). Several forms of TCV were developed, including the administration of T cell lines attenuated by irradiation or mitomycin C, membrane modified cells and sub-pathogenic doses of unmodified T cells. The vaccinating effect was found to be mediated by T cells. Vaccinated animals had both CD4 T cells that responded to the vaccine and CD8 T cells that suppressed its response to the autoantigen. The major obstacle to the clinical application of TCV in human autoimmune diseases is the fact that the nature of autoantigens initiating and perpetuating the disease are not known.