gebhart/patrepeval huggingface dataset:
Access of the Substrate to the Active Site of Yeast Oxidosqualene Cyclase: An Inhibition and Site‐Directed Mutagenesis Approach (2005)

A structural model of Saccharomyces cerevisiae oxidosqualene cyclase (SceOSC) suggests that some residues of the conserved sequence Pro-Ala-Glu-Val-Phe-Gly (residues 524-529) belong to a channel constriction that gives access to the active-site cavity. Starting from the SceOSC C457D mutant, which lacks the cysteine residue next to the catalytic Asp456 residue Cys457 has been replaced but Asp456 is still there, we prepared two further mutants where the wild-type residues Ala525 and Glu526 were individually replaced by cysteine. These mutants, especially E526C, were very sensitive to the thiol-reacting agent dodecyl-maleimide. Moreover, both the specific activity and the thermal stability of E526C were severely reduced. A similar decrease of the enzyme functionality was obtained by replacing Glu526 with alanine, while substitution with the conservative residues aspartate or glutamine did not alter catalytic activity. Molecular modeling of the yeast wild-type OSC and mutants on the template structure of human OSC confirms that the channel constriction is an important aspect of the protein structure and suggests a critical structural role for Glu526.
Risk factors for progressive cartilage loss in the knee (2002)

MRI can detect interval cartilage loss in patients over a short period (<2 years). The presence of meniscal and ACL tears was associated with more rapid cartilage loss. Cartilage lesions located in the central region of the medial compartment showed more rapid progression of cartilage loss than cartilage lesions in the anterior and posterior portions of the medial compartment. The findings in this study suggest that patients entering clinical trials investigating antiarthritis regimens may need to be randomized based on location of the lesion.
Figure S2 from TRK Fusions Are Enriched in Cancers with Uncommon Histologies and the Absence of Canonical Driver Mutations (2023)

&lt;p&gt;Supplemental Figure 2. Age Distribution of Patients in the MSK TRK Cohort.&lt;/p&gt;
Heart Rate Estimation Algorithm From Wrist-based Photoplethysmogram Using Subspace Learning Method (2019)

Wrist based devices, like smart-watches, fitness bands and health monitors all provide a common sensor called Photoplethysmography (PPG) to measure optical pulse signal. This is usually used to derive the instantaneous heart-rate (HR), which is useful while doing any exercise or to monitor on a regular basis for chronic patients. However, one major issue with the signal is that it is easily corrupted by ambulatory motion generated by hand movements of the subject. Since, these devices also come equipped with an independent motion sensor, namely a tri-axes accelerometer, researchers have taken interest in trying to correct the motion artifact in PPG using the accelerometer as a reference noise signal. However, it is not a trivial problem and hence, even after a substantial body of research, the problem remains unsolved, especially when considering on-premise estimation due to the resource-constrained nature of wearable devices. In this paper, we aim to solve this problem using subspace based learning approach. Though this approach has been utilized before, we have added some novel steps to the algorithm pipeline and also made modifications so that the algorithm can be possibly run on a typical wearable device. Our preliminary results show efficacy and promise of our proposed approach.
A 25 Gb/s Hybrid-Integrated Silicon Photonic Source-Synchronous Receiver With Microring Wavelength Stabilization (2016)

Single-mode wavelength-division multiplexing (WDM) optical links are an attractive technology to meet the growing interconnect bandwidth demand in data center applications. This paper presents a multi-channel hybrid-integrated photonic receiver based on microring drop filters and waveguide photodetectors implemented in a 130 nm SOI process and high-speed optical front-ends designed in 65 nm CMOS. The source-synchronous receiver utilizes an LC injection-locked oscillator (ILO) in the clock path for improved jitter filtering, while maintaining correlated jitter tracking with the data channels. Receiver sensitivity is improved with a large input-stage feedback resistor transimpedance amplifier (TIA) cascaded with an adaptively-tuned continuous-time linear equalizer (CTLE). In order to stabilize the microring drop filter resonance wavelength, a peak-detector-based thermal tuning loop is implemented with a 0.7 nm range at <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$43~\mu \text {W}$ </tex-math></inline-formula> /GHz efficiency. When tested with a waveguide photodetector with 0.45 A/W responsivity, the receiver achieves -8.0 dBm OMA sensitivity at a BER <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$= 10^{\mathrm {-12}}$ </tex-math></inline-formula> with a jitter tolerance corner frequency near 20 MHz and a per-channel power consumption of 17 mW including amortized clocking power.
Effect of heart rate on the canine end-systolic pressure-volume relationship. (1985)

Although the rate dependence of isolated muscle contractility is well known, the ventricular end-systolic pressure-volume relationship (ESPVR) has been reported to be insensitive to heart rate. To resolve this contradiction, we used an isolated, ejecting canine heart preparation perfused at a constant coronary arterial pressure. Heart rate was changed from 60 to 200 beats/min in steps of 20 beats/min. At least 10 pressure-volume loops under different filling pressures were obtained at each heart rate in each of six hearts. Over a heart rate range from 60 to 120 beats/min, the slope of the ESPVR (Ees) increased significantly from 3.5 +/- 0.4 (SE) to 5.3 +/- 0.6 mm Hg/ml. In the range between 120 and 180 beats/min there was little change in Ees (5.3 +/- 0.6 to 5.4 +/- 0.6 mm Hg/ml), but at 200 beats/min Ees increased slightly to 5.7 +/- 0.5 mm Hg/ml. The volume axis intercept (V0) of the ESPVR changed little over the range of heart rate from 60 to 160 beats/min (10.2 +/- 2 ml to 9.4 +/- 1.3 ml) but increased to 15.2 +/- 1.2 ml at a rate of 200 beats/min. The change in ESPVR with increase in heart rate from 60 to 120 beats/min (i.e., increase in Ees without change in V0) is the same as those seen with a positive inotropic intervention with calcium or cathecholamines, whereas the V0 changes over the range from 160 to 200 beats/min is similar to those seen with regional ischemia.(ABSTRACT TRUNCATED AT 250 WORDS)
Global memory optimisation for embedded systems allowed by code duplication (2005)

The data transfers and storage are dominating contributors to the area and power consumption for all modern multimedia embedded systems. Modern high-level memory optimisations can ensure cost-efficient realisation of these systems. An important step in these optimisations are loop transformations performed on a geometrical model. However, these loop transformations traditionally cannot optimise code across data dependent conditions.In this paper we selectively duplicate the code in order to enable global loop transformations across data dependent conditions. We propose a technique which finds in a systematic way the Pareto curve in 2D exploration space: the better memory optimisations vs. the code increase. Our technique has been tested on an MP3 audio decoder. Results show 45.8% decrease in the number of main memory accesses which requires a 16.2% increase of code size.
Preclinical biomarkers for a cyclin-dependent kinase inhibitor translate to candidate pharmacodynamic biomarkers in phase I patients (2009)

A genomics-based approach to identify pharmacodynamic biomarkers was used for a cyclin-dependent kinase inhibitory drug. R547 is a potent cyclin-dependent kinase inhibitor with a potent antiproliferative effect at pharmacologically relevant doses and is currently in phase I clinical trials. Using preclinical data derived from microarray experiments, we identified pharmacodynamic biomarkers to test in blood samples from patients in clinical trials. These candidate biomarkers were chosen based on several criteria: relevance to the mechanism of action of R547, dose responsiveness in preclinical models, and measurable expression in blood samples. We identified 26 potential biomarkers of R547 action and tested their clinical validity in patient blood samples by quantitative real-time PCR analysis. Based on the results, eight genes (FLJ44342, CD86, EGR1, MKI67, CCNB1, JUN, HEXIM1, and PFAAP5) were selected as dose-responsive pharmacodynamic biomarkers for phase II clinical trials.
Interaction of H2O with active Spindt-type molybdenum field emitter arrays (1999)

Electron emission from molybdenum field emission microcathode arrays is sensitive to the contamination of the emitters by the residual gases. We studied the effects of H2O exposures on the emission properties of several Spindt-type molybdenum field emitter arrays. Exposure of the field emitters to H2O resulted in emission degradation ranging from (13.8±5.7)% for 50 L to 90.7% for a 4000 L exposure.
Key hardware components of a cardiac-enabled CT scanner (2022)

Abstract Awareness of a few basic hardware components of a CT scanner is key for the delivery of cardiac CT in clinical practice. Contemporary CT scanners comprise a rotating gantry onto which are housed the X-ray tube(s) and the detector array(s). Collimators determine the shape of the emitted X-ray beam to maximize image quality and minimize radiation exposure to patients. Detectors receive and transform the signal necessary to reconstruct CT images of multiple sections of the patient’s anatomy. The term ‘multidetector’ or ‘multislice’ CT refers to the ability to image multiple sections of the patient’s anatomy along the z-axis during one gantry rotation. Single-source CT systems contain one X-ray tube and one detector array; ‘dual-source’ CT contains two X-ray sources coupled with two detector arrays mounted at an (approximately) 90-degree angle. Dual-source CT allows halving of the temporal resolution compared to a single-source system with the same gantry rotation time. A motorized scanner table, the ECG synchronization system, and a power injection are further key requirements to deliver cardiac CT in the clinical arena.
A common variant near TGFBR3 is associated with primary open angle glaucoma (2015)

Primary open angle glaucoma (POAG), a major cause of blindness worldwide, is a complex disease with a significant genetic contribution. We performed Exome Array (Illumina) analysis on 3504 POAG cases and 9746 controls with replication of the most significant findings in 9173 POAG cases and 26 780 controls across 18 collections of Asian, African and European descent. Apart from confirming strong evidence of association at CDKN2B-AS1 (rs2157719 [G], odds ratio [OR] = 0.71, P = 2.81 × 10(-33)), we observed one SNP showing significant association to POAG (CDC7-TGFBR3 rs1192415, ORG-allele = 1.13, Pmeta = 1.60 × 10(-8)). This particular SNP has previously been shown to be strongly associated with optic disc area and vertical cup-to-disc ratio, which are regarded as glaucoma-related quantitative traits. Our study now extends this by directly implicating it in POAG disease pathogenesis.
Supplementary Figure 1 from Efficacious Immune Therapy in Chronic Myelogenous Leukemia (CML) Recognizes Antigens That Are Expressed on CML Progenitor Cells (2023)

Supplementary Figure 1 from Efficacious Immune Therapy in Chronic Myelogenous Leukemia (CML) Recognizes Antigens That Are Expressed on CML Progenitor Cells
Tailoring the Swelling Pressure of Degrading Dextran Hydroxyethyl Methacrylate Hydrogels (2003)

Swelling pressure measurements were performed on degrading dextran hydroxyethyl methacrylate (dex-HEMA) hydrogels. In these networks, the cross-links are hydrolyzable carbonate ester bonds formed between methacrylate groups and dextran molecules. It is demonstrated that dex-HEMA gels made in the presence of a known amount of free dextran chains exhibit osmotic properties similar to those of partially degraded dex-HEMA gels. The swelling pressure, Πsw, of degrading dex-HEMA gels is controlled primarily by the cross-linked dex-HEMA polymer and the free dextran molecules, while the contribution of short poly-HEMA fragments (produced in the degradation process) is negligible. It is found that Πsw only slightly changes during the first 15 days of degradation. Close to the end of the degradation process, however, a much faster increase in Πsw is observed. The swelling pressure profile of these gels strongly depends on the concentration of the cross-linked dex-HEMA and its chemical composition (amount of HEMA groups per 100 glucose units).
246 Classification of Eigenmodes for Efficient Analysis Based on Similarity among Change of FRF peaks (2006)

Observing each vibration mode is a basic and useful approach for automobile NVH in the booming noise frequency range. In the recent vibration analysis, the number of modes in the target frequency range increases as the finite element model reflects an actual automobile faithfully. In this case, it's difficult to examine individual mode, and it is required a lot of time to establish effective countermeasures. In this study, a practical method is proposed to raise the efficiency of analysis by grouping these modes into several types. The types are defined by the similarity of the effects of modifications that are made on noticed portions of the structure. The grouping method enables the analyst to effectively draw countermeasures for each group and reduces the analysis time.
Methyl vinyl glycolate as a diverse platform molecule (2016)

Methyl vinyl glycolate (MVG) is available by zeolite catalyzed degradation of sugars and constitutes a precursor to industrially promising structures by homo metathesis, cross metathesis, Claisen-type rearrangements and allylic alcohol transposition.
ChemInform Abstract: CYCLIZATION REACTION OF N‐SUBSTITUTED MANDELHYDRAZIDE WITH FORMALDEHYDE (1978)

Abstract Aus Mandelsäuremethylester (I) und den Hydrazinen (II) werden die Hydrazide (III) in meist guten Ausbeuten erhalten.
Polytetrahydrofuran Cross-Linked Polystyrene Resins for Solid-Phase Organic Synthesis (2000)

Currently, divinylbenzene cross-linked polystyrene (DVB-PS) is the polymer of choice for use in solid-phase organic synthesis (SPOS). While much research has been directed toward the optimization of linker groups for the attachment of compounds to the polymer, the development of new polymers themselves has been relatively neglected. In an attempt to overcome the shortcomings of DVB-PS and to develop new polymers with optimum properties for use in organic synthesis, we have prepared a series of polystyrene polymers that incorporate flexible polytetrahydrofuran (PTHF) based cross-linkers. The objective of incorporating PTHF into the polymers was to slightly increase the overall polarity of the polymer and thus render the resins more organic solvent-like. Since the degree to which a resin swells in and absorbs a particular solvent correlates to how well substrates attached to the polymer are solvated, we compared the swelling of our new resins to commercially available DVB-PS resins. In all cases, we found that our resins swelled to a much greater extent than do DVB-PS resins, and their use should therefore allow for SPOS reaction conditions that more closely mimic homogeneous solution-phase conditions. It was also found that the PTHF chain length of the cross-linker does not affect the level of swelling since all of our cross-linkers afford resins with comparable levels of increased swelling. Furthermore, we have examined the utility of our resins in directed ortho-metalation reactions and found that the increased swelling of our resins allows for isolation of reaction products in yields comparable to what is achieved using standard solution-phase conditions.
Lamellae-controlled electrical properties of polyethylene – morphology, oxidation and effects of antioxidant on the DC conductivity (2020)

Destruction of the spherulite structure in low-density polyethylene (LDPE) is shown to result in a more insulating material at low temperatures, while the reverse effect is observed at high temperatures. On average, the change in morphology reduced the conductivity by a factor of 4, but this morphology-related decrease in conductivity was relatively small compared with the conductivity drop of more than 2 decades that was observed after slight oxidation of the LDPE (at 25 °C and 30 kV mm<sup>-1</sup>). The conductivity of LDPE was measured at different temperatures (25-60 °C) and at different electrical field strengths (3.3-30 kV mm<sup>-1</sup>) for multiple samples with a total crystalline content of 51 wt%. The transformation from a 5 μm coherent structure of spherulites in the LDPE to an evenly dispersed random lamellar phase (with retained crystallinity) was achieved by extrusion melt processing. The addition of 50 ppm commercial phenolic antioxidant to the LDPE matrix (<i>e.g.</i> for the long-term use of polyethylene in high voltage direct current (HVDC) cables) gave a conductivity <i>ca.</i> 3 times higher than that of the same material without antioxidants at 60 °C (the operating temperature for the cables). For larger amounts of antioxidant up to 1000 ppm, the DC conductivity remained stable at <i>ca.</i> 1 × 10<sup>-14</sup> S m<sup>-1</sup>. Finite element modeling (FEM) simulations were carried out to model the phenomena observed, and the results suggested that the higher conductivity of the spherulite-containing LDPE stems from the displacement and increased presence of polymeric irregularities (formed during crystallization) in the border regions of the spherulite structures.
Reproducible Quantification of the Microstructure of Complex Quenched and Quenched and Tempered Steels Using Modern Methods of Machine Learning (2023)

Current conventional methods of evaluating microstructures are characterized by a high degree of subjectivity and a lack of reproducibility. Modern machine learning (ML) approaches have already shown great potential in overcoming these challenges. Once trained with representative data in combination with objective ground truth, the ML model is able to perform a task properly in a reproducible and automated manner. However, in highly complex use cases, it is often not possible to create a definite ground truth. This study addresses this problem using the underlying showcase of microstructures of highly complex quenched and quenched and tempered (Q/QT) steels. A patch-wise classification approach combined with a sliding window technique provides a solution for segmenting entire microphotographs where pixel-wise segmentation is not applicable since it is hardly feasible to create reproducible training masks. Using correlative microscopy, consisting of light optical microscope (LOM) and scanning electron microscope (SEM) micrographs, as well as corresponding data from electron backscatter diffraction (EBSD), a training dataset of reference states that covers a wide range of microstructures was acquired in order to train accurate and robust ML models in order to classify LOM or SEM images. Despite the enormous complexity associated with the steels treated here, classification accuracies of 88.8% in the case of LOM images and 93.7% for high-resolution SEM images were achieved. These high accuracies are close to super-human performance, especially in consideration of the reproducibility of the automated ML approaches compared to conventional methods based on subjective evaluations through experts.
There Ain’t No Such Thing as a Free Custom Memory Allocator (2022)

Using custom memory allocators is an efficient performance optimization technique. However, dependency on a custom allocator can introduce several maintenance-related issues. We present lessons learned from the industry and provide critical guidance for using custom memory allocators and enumerate various challenges associated with integrating them. These recommendations are based on years of experience incorporating custom allocators into different industrial software projects.
Error resilience of EZW coder for image transmission in lossy networks (2003)

We investigate the effect of network errors on Embedded Zerotree Wavelet (EZW) encoded images and propose modifications to the EZW coder to increase error resilience in bursty packet loss conditions. A hybrid-encoding scheme that uses data interleaving to spread correlated information into independently processed groups and layered encoding to protect significant information within each group is presented. Simulation results for various packet loss percentages show the improved error resiliency of our scheme in random and bursty packet loss environments.
Mortality and Cerebrovascular Events After Heart Rhythm Disorder Management Procedures (2017)

Half of the deaths directly related to an HRDM procedure were among the patients undergoing device implantation procedures, with cardiac tamponade being the most common cause of death. This highlights the importance of the development of protocols for the quick identification and management of cardiac tamponade even in procedures typically believed to be lower risk such as device implantation.
Influence of near-field electromagnetic interactions on optical properties of perfect lens consisting of left-handed material (2005)

In this paper, we investigate the surface plasma resonance of a slab of left-handed material (LHM). We use the transfer matrix method to calculate the attenuated total reflection spectra of the LHM slab. The intrinsic parameters of the LHM slab are suitable chose so that the slab has both negative permittivity and permeability in a frequency range of visible light. We have calculated the cases with different slab thickness and various dielectrics surrounding the LHM slab.
Discrete time point to point position control of a system with actuator saturation (2005)

A method for developing a controller for point to point positioning of a single degree of freedom system with significant actuator saturation effects is developed and experimental results are presented. This method involves identifying the maximum stopping capacity of the actuator as a function of velocity and using this information to define a limiting state space trajectory associated with the fastest achievable deceleration and to compute a state to input mapping that will direct the system near to this limiting trajectory via discrete time control. The chief motivation for this work is to provide a simple, direct method to identify the crucial actuator limitation of a positioning system and use that information directly to achieve near minimum time point to point motion control despite significant nonlinear actuator characteristics. Experiments were conducted on a suitable system to verify the effectiveness of this technique and results are presented. This technique can also handle payload uncertainties easily and effectively.
The antioxidant properties of non stroidal anti-inflammatory drugs (2000)

peer reviewed